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The ingestion of cold water in winter results in fluctuating decreases in rumen temperature, impacting rumen fermentation function and methane production. This study aimed to investigate the impact of calcium propionate (CaP) on rumen fermentation characteristics, methane production, and microbial microbiome under different in vitro incubation temperatures. A 2 × 2 factorial experiment was conducted over 72 h, with or without 2.5% CaP (dry matter [DM] basis) in substrate under a constant incubation temperature (39 °C, CIT) or shifting incubation temperatures (12 cycles in total, with each cycle consisting of 4 h of incubation at 39 °C followed by immediate transfer to 30 °C for 2 h, ITS). The results showed that ITS inhibited the gas production, methane production, and methane concentration at 12 and 72 h (p < 0.05), and reduced the concentration of ammonium nitrogen (−14.25%), propionate (−16.14%), butyrate (−12.67%), and total volatile fatty acid (−8.50%) at 72 h more than the CIT groups (p < 0.05). The addition of 2.5% CaP significantly increased the gas production at 72 h (+4.84%), asymptotic gas production (+5.08%, per 0.2 g DM substrate), concentration of propionate (+18.05%), and valerate (+9.45%) (p < 0.05) compared to CaP-free groups, while it had no observable effect on the production or concentration of methane. Furthermore, the addition of 2.5% CaP yielded a significant increase in the relative abundance of Bacteroides (p < 0.05). Under the ITS condition, the relative abundance of Methanomicrobiales decreased and was positively correlated with methane production at 72 h (r = 0.47, p < 0.05). Additionally, CaP decreased the abundance of Prevotella_UCG_003 (p < 0.05), which was negatively correlated with the asymptotic gas production (r = 0.45, p < 0.05). Overall, our study suggests that the addition of 2.5% CaP can alleviate the adverse effects of ITS on in vitro fermentation parameters by regulating microbial composition and sustaining a reduction in methane production.

In tropical regions, the patterns of carbon (C) and nutrient properties among ecosystems dominated by distinct mycorrhizal associations are unknown. We aim to reveal whether the dynamics differ and the ecological drivers and ecosystem functioning implications of such differences. Based on a dataset of 97 tropical forest sites, we related EcM trees abundance (as a proxy for the transition from AM to EcM trees dominance) to different topsoil properties, climatic conditions and microbial abundance proxies through Generalized Additive Models. Higher abundances of EcM trees were correlated with higher topsoil concentrations of total nitrogen and C, extractable phosphorus and potassium, delta C-13, mean annual temperature, precipitation, microbial (bacterial and fungal) biomass and the relative abundance of saprotrophic fungi. Synthesis. Our results reveal consistent differences in carbon and nutrient content between arbuscular mycorrhizal (AM-) and EcM-dominated vegetation across the tropical biome, pointing to lower soil fertility and lower rates of C and nutrient transformation processes in EcM-dominated forests. These patterns associate with lower topsoil C accumulation when compared to AM vegetation, which contrasts with patterns reported for temperate forests. We suggest that different mechanisms of soil organic matter accumulation explain the contrasting impacts of EcM dominance on topsoil properties of temperate and tropical biomes. Global vegetation and C models should account for the contrasting impacts of distinct mycorrhizal vegetation in different climatic zones. Stichting voor de Technische Wetenschappen [016.161.318]

Polar marine environments host a complex assemblage of cold-adapted auto- and heterotrophic microorganisms that affect water biogeochemistry and ecosystem functions. However, due to logistical difficulties, remote regions like those in close proximity to glaciers have received little attention, resulting in a paucity of microbiological data. To fill these gaps and obtain novel insights into microbial structure and function in Arctic regions, a survey of microbial communities in an area close to the Blomstrandbreen glacier in Kongsfjorden (Svalbard Archipelago; Arctic Ocean) was carried out during an early summer period. An Unmanned Autonomous Vehicle designed to safely obtain seawater samples from offshore-glacier transects (PROTEUS, Portable RObotic Technology for Unmanned Surveys) was equipped with an automatic remotely-controlled water multi-sampler so that it could sample just beneath the glacier, where access from the sea is difficult and dangerous. The samples were analysed by image analysis for the abundance of total prokaryotes, viable and respiring cells, their morphological traits and biomass; by flow cytometry for autotrophic and prokaryotic cells (with high and low nucleic acid contents) as well as virus-like particle counts; by BIOLOG ECOPLATES for potential community metabolism; and by fluorimetry for potential enzymatic activity rates on organic polymers. Contextually, the main physical and chemical (temperature, salinity, pH, dissolved oxygen and nutrients) parameters were detected. Altogether, besides the PROTEUS vehicle’s suitability for collecting samples from otherwise inaccessible sites, the multivariate analysis of the overall dataset allowed the identification of three main sub-regions differently affected by the haline gradient (close to the glacier) or terrigenous inputs coming from the coast. A complex microbiological scenario was depicted by different patterns of microbial abundance and metabolism among the transects, suggesting that ice melting and Atlantic water inflow differently supported microbial growth.

It is of interest to study the rhizobacteria associated with two different desert wild plants, e.g., Calotropis procera and Senna alexandrina compared with bulk soil sample in order to identify signatures of microbes in rhizospheres of the two plants and detect influence of soil microbiome in drawing soil architecture. Analysis of deep sequencing microbial dataset indicated occurrence of 296,642 sequence tags assigned 5,210 OTUs (operational taxonomic units). Species richness in control sample was higher than those of either plant's rhizosphere, while microbial abundance was lower. Principal coordinate analysis (PCoA) plot indicated complete separation of microbiome diversity among groups. Abundances of Pseudomonas stutzeri and Virgibacillus koreensis increased in the rhizosphere of C. procera compared with that of S. alexandrina, while those of Streptococcus sobrinus, Veillonella parvula and unassigned species of Sphingomonas genus increased in rhizosphere of S. alexandrina. Unassigned species of genera Marinobacter, Porticoccus and Alcanivorax only exist in rhizosphere microbiome of C. procera, while unassigned species of genus Pseudomonas only exists in rhizosphere microbiome of Senna alexandrina. High abundances of the two microbes Pseudomonas stutzeri and Virgibacillus koreensis in rhizosphere of C. procera allow the plant to grow well under both normal and saline condition. Also, Marinobacter, Porticoccus and Alcanivorax genera only exist in rhizosphere microbiome of C. procera. These microbes produce siderophores that protect plant from pathogens. Data shows that C. procera might be more protected from microbial pathogens compared with S. alexandrina. The differential abundances or exclusive presence of soil microbes reflect the ability of plant species to survive under biotic and abiotic stresses. Results imply that rhizospheric microbes can be used as biomarkers of plant growth rate and the ability to survive under harsh conditions.

Gynosaponin is known to modulate rumen methanogenesis and microbial fermentation characteristics in ruminants. The current experiment aimed to determine the time-dependent effects of intraruminal polymeric media-coated gynosaponin (PMCG) supplementation on the methanogenesis, rumen fermentation properties and microbial abundance in Xinjiang goats. Eight goats were used in a 2 × 2 crossover arrangement with a PMCG group (8 g/kg DMI) and a control group (0 g/kg DMI). The experiment was divided into four phases, each lasted 21 d. Ruminal contents were obtained for analysis of rumen fermentation properties and microbial abundance. Protozoa numbers were counted by microscope and the abundance of methanogens, rumen fungi and cellulolytic bacteria were quantified by real-time PCR. The results indicated that PMCG significantly reduced methane production (p < 0.05) during the first two phases but this increased to baseline again during the last two phases. Meanwhile, the concentration of acetate decreased remarkably, which resulted in a significant reduction in the acetate to propionate ratio and total VFA concentration (p < 0.05). However, other rumen properties and dry matter intake were not affected (p > 0.05). During the first and second phases, the protozoa numbers and gene copies of methanogens, total bacteria and F. succinogens relative to the 16 s rDNA were all slightly decreased, but the statistical results were not significant. However, the ruminal supplementation of PMCG had little effect on other tested microbes. Accordingly, it was concluded that the addition of PMCG had an inhibitory effect on methane production probably due to a decline in methanogen numbers.

Rice is an important source of methane (CH4) and other crops may be sources of nitrous oxide (N2O), both of which are powerful greenhouse gases. In Uruguay, irrigated rice rotates with perennial pastures and allows high productivity and low environmental impact. A long-term experiment with contrasting rice rotation intensification alternatives, including rice–soybean and continuous rice, was recently carried out in an Argialboll located in a temperate region of South America. To know if rotation systems influence soil microbial activity involved in CH4 and N2O emissions, the abundance and potential rate for gas production or consumption of microbial populations were measured during the rice crop season. CH4 was only emitted when rice was flooded and N2O emission was not detected. All rotational soils showed the highest rate for methanogenesis at tillering (30 days after rice emergence), while for methanotrophy, the maximum rate was reached at flowering. The abundance of related genes also followed a seasonal pattern with highest densities of mcrA genes being observed at rice flowering whereas pmoA genes were more abundant in dry soils after rice harvest, regardless of the rotation system. Differences were found mainly at tillering when soils with two consecutive summers under rice showed higher amounts of mcrA and pmoA gene copies. The potential denitrification rate was highest at the tillering stage, but the abundance of nirK and nirS genes was highest in winter. Regarding ammonium oxidation, bacterial amoA abundance was higher in winter while the archaeal amoA gene was similar throughout the year. A strong influence of the rice growth stage was registered for most of the parameters measured in rice paddy soils in this no-till rice intensification experiment. However, differences among rotations begin to be observed mainly at tillering when the abundance of populations of the methane and nitrous oxide cycles seemed to respond to the rice intensification.

Plants and microorganisms, besides the climate, drive nitrogen (N) cycling in ecosystems. Our objective was to investigate N losses and N acquisition strategies along a unique ecosystem-sequence (ecosequence) ranging from arid shrubland through Mediterranean woodland to temperate rainforest. These ecosystems differ in mean annual precipitation, mean annual temperate, and vegetation cover, but developed on similar granitoid soil parent material, were addressed using a combination of molecular biology and soil biogeochemical tools. Soil N and carbon (C) contents, δ15N signatures, activities of N acquiring extracellular enzymes as well as the abundance of soil bacteria and fungi, and diazotrophs in bulk topsoil and rhizosphere were determined. Relative fungal abundance in the rhizosphere was higher under woodland and forest than under shrubland. This indicates toward plants' higher C investment into fungi in the Mediterranean and temperate rainforest sites than in the arid site. Fungi are likely to decompose lignified forest litter for efficient recycling of litter-derived N and further nutrients. Rhizosphere—a hotspot for the N fixation—was enriched in diazotrophs (factor 8 to 16 in comparison to bulk topsoil) emphasizing the general importance of root/microbe association in N cycle. These results show that the temperate rainforest is an N acquiring ecosystem, whereas N in the arid shrubland is strongly recycled. Simultaneously, the strongest 15N enrichment with decreasing N content with depth was detected in the Mediterranean woodland, indicating that N mineralization and loss is highest (and likely the fastest) in the woodland across the continental transect. Higher relative aminopeptidase activities in the woodland than in the forest enabled a fast N mineralization. Relative aminopeptidase activities were highest in the arid shrubland. The highest absolute chitinase activities were observed in the forest. This likely demonstrates that (a) plants and microorganisms in the arid shrubland invest largely into mobilization and reutilization of organically bound N by exoenzymes, and (b) that the ecosystem N nutrition shifts from a peptide-based N in the arid shrubland to a peptide- and chitin-based N nutrition in the temperate rainforest, where the high N demand is complemented by intensive N fixation in the rhizosphere.

Savremena poljoprivredna proizvodnja podrazumeva neracionalnu upotrebu velikih količina pesticida, što narušava kvalitet i plodnost poljoprivrednih zemljišta. Visoke koncentracije teških metala u zemljištu predstavljaju veliki rizik po agroekosisteme i živi svet, a najčešći uzrok zagađenja je antropogeni uticaj i neadekvatna primena hemijskih sredstava. Usled dugotrajne i intenzivne primene fungicida na bazi bakra, zemljišta pod vinogradima posebno su ugrožena od zagađenja ovim metalom. Primena fungicida na bazi bakra, često je povezana sa smanjenom aktivnošću mikroorganizama i promenama u strukturi mikrobnih zajednica. U cilju globalne procene stanja zemljišta pod vinogradima ispitane su fizičke, hemijske i mikrobiološke osobine zemljišta i u vinogradarskom rejonu Vranje. Brojnost mikroorganizama i dehidrogenazna aktivnost u uzorcima sa kontrolnih parcela ukazuju da način iskorišćenja parcele nije uticao na mikrobiološke parametre zemljišta. Raznovrsnost, brojnost i aktivnost mikroorganizama zavisili su prvenstveno od pH reakcije i fizičko-hemijskih osobina zemljišta. Modern agricultural production implies irrational use of large amounts of pesticides, which impairs the quality and fertility of agricultural soil. High concentrations of heavy metals in the soil pose a great risk to agroecosystems and wildlife, and the most common cause of pollution is anthropogenic impact and inadequate use of chemicals. Due to long-term and intensive application of copper-based fungicides, soils under vineyards is particularly vulnerable to pollution by this metal. The use of copper-based fungicides is often associated with reduced activity of microorganisms and changes in the structure of microbial communities. In order to globally assess the condition of the soil under vineyards physical, chemical and microbiological properties of the soil in the wine-growing region of Vranje were examined. The abundance of microorganisms and dehydrogenase activity in the control plots indicate that the method of plot utilization did not affect the microbiological parameters of the soil. The diversity, abundance and activity of microorganisms depended primarily on the pH reaction and physical and chemical properties of the soil.

Efficient water treatment is required to maintain high water quality and control microbial growth in recirculating aquaculture systems (RAS). Here, we examined the effects of two treatment methods, ozonation and foam fractionation, separately and combined, on the microbiology in twelve identical experimental RAS with rainbow trout (Oncorhyncus mykiss) during 8 weeks. Microbes suspended in water and growing in biofilter biofilms were examined using flow cytometry analysis and high throughput sequencing of the 16S rRNA gene. The results showed that foam fractionation did not cause large changes in abundance or overall community composition of free-living microbes. Instead, through decreasing the organic matter availability in water, it targeted specific microbial taxa, leading to e.g. decreased potential for off-flavor production. In contrast, ozonation was found to have a profound impact on the system microbiology, by reducing the overall cell abundance, increasing microbial dead/live ratio, and changing the community composition of both free-living and biofilm microbes. Ozonation increased the abundance of certain key microbial taxa adapted to low carbon conditions, which might form a stable and more abundant community under a prolonged ozone dosing. Combining the two treatment methods did not provide any additional benefits as compared to ozonation solely, corroborating the high disinfection potential of ozone. However, ozone had only a minor impact on biofilter microbial communities, which were, in general, more resistant to water treatment than water communities. Water treatment had no effect on the overall genetic nitrification potential in the biofilter biofilms. However, foam fractionation led to changes in the nitrifying microbial community in biofilter, increasing the abundance of Nitrospira conducting complete ammonia oxidation to nitrate (comammox). Altogether, the results obtained indicate that although these two water treatment methods have similar outcomes on physico-chemical water quality and microbial activity, their underlying mechanisms are different, potentially leading to different outcomes under the long-term application.

The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.

Microbial communities are known to be sensitive indicators for water pollution and biomonitoring assessment. In this study, we aimed at observation of microbial abundance and community composition in the mountain river Morávka. The results showed temporal and spatial changes in total cell abundance (TCA). TCA reached 105–106 cells/ml, increasing values were detected towards the mouth with maxima in summer and autumn months. Out of Eubacteria Betaproteobacteria and Cytophaga-Flavobacterium were found to predominate, while Archaea represented only 4.8 % of TCA. Along the flow three distinct patterns of phylogenetic groups' share were revealed related to increasing pollution. Microbial community composition was found to be most significantly dependent on the elevation and the sampling date. Moreover, environmental variables like O2 saturation, water temperature, trophic potential and pH influenced microbial community as well. Statistical analyses showed significant seasonal (23.5 %) and spatial (4.7 %) changes in microbial community composition.

The aim of the study was to examine the effects of management practice on microbial properties of soil under soybean production. The study included 180 samples of soil under certified organic soybean production and 80 samples in conventional production system. An abundance of the examined microbial groups was assessed using the indirect dilution method, followed by plating of soil suspension on different selective media, while dehydrogenase and β-glucosidase activity was measured spectrophotometrically. Our data indicated that the management practice affected the structure and activity of microbial com­munities. A significant positive effect of organic farming on Azotobacter spp., free N-fixers and abundance of actinomycetes was identified. The influence of management system for the total number of bacteria, ammonifiers and fungi was not observed. Significantly higher dehydrogenase and β-glucosidase activity was recorded in the soils under organic farming compared to the conventional farming. The obtained results showed an increase in organic matter content, associated with organic soil management, and its positive correlation with soil microbial properties. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. TR 30122]

Objective The objective of this study was to investigate the effects of essential oil mixture (EOM) supplementation on rumen fermentation characteristics and microbial changes in an in vitro. Methods Three experimental treatments were used: control (CON, no additive), EOM 0.1 (supplementation of 1 g EOM/kg of substrate), and EOM 0.2 (supplementation of 2 g EOM/kg of substrate). An in vitro fermentation experiment was carried out using strained rumen fluid for 12 and 24 h incubation periods. At each time point, in vitro dry matter digestibility (IVDMD), neutral detergent fiber digestibility (IVNDFD), pH, ammonia nitrogen (NH3-N), and volatile fatty acid (VFA) concentrations, and relative microbial diversity were estimated. Results After 24 h incubation, treatments involving EOM supplementation led to significantly higher IVDMD (treatments and quadratic effect; p = 0.019 and 0.008) and IVNDFD (linear effect; p = 0.068) than did the CON treatment. The EOM 0.2 supplementation group had the highest NH3-N concentration (treatments; p = 0.032). Both EOM supplementations did not affect total VFA concentration and the proportion of individual VFAs; however, total VFA tended to increase in EOM supplementation groups, after 12 h incubation (linear; p = 0.071). Relative protozoa abundance significantly increased following EOM supplementation (treatments, p

Objective The objective of this study was to investigate the effects of essential oil mixture (EOM) supplementation on rumen fermentation characteristics and microbial changes in an in vitro. Methods Three experimental treatments were used: control (CON, no additive), EOM 0.1 (supplementation of 1 g EOM/kg of substrate), and EOM 0.2 (supplementation of 2 g EOM/kg of substrate). An in vitro fermentation experiment was carried out using strained rumen fluid for 12 and 24 h incubation periods. At each time point, in vitro dry matter digestibility (IVDMD), neutral detergent fiber digestibility (IVNDFD), pH, ammonia nitrogen (NH3-N), and volatile fatty acid (VFA) concentrations, and relative microbial diversity were estimated. Results After 24 h incubation, treatments involving EOM supplementation led to significantly higher IVDMD (treatments and quadratic effect; p = 0.019 and 0.008) and IVNDFD (linear effect; p = 0.068) than did the CON treatment. The EOM 0.2 supplementation group had the highest NH3-N concentration (treatments; p = 0.032). Both EOM supplementations did not affect total VFA concentration and the proportion of individual VFAs; however, total VFA tended to increase in EOM supplementation groups, after 12 h incubation (linear; p = 0.071). Relative protozoa abundance significantly increased following EOM supplementation (treatments, p

13 páginas.- 3 figuras.- 1 tabla.- referencias, Sulfur (S) is a macro-element required for life. S deficiency limits plant growth. Microorganisms carry out several essential steps in the recycling of organic and inorganic S in soils. Microbes and plants interact, mainly in the rhizosphere, but the mechanisms ruling these interactions and the extent of such relationships remain poorly understood. Here, we update current perspectives on the role of specific microorganisms involved in S cycling and the spatial interaction between plants and microbes. To contextualize the pitfalls of current approaches in studying soil S transformations, we review the current main established steps, redox reactions and microbial players in the S cycle. The incorporation of novel microbial taxa, namely those important for organic S mineralization, which may be important ecosystem players in terms of soil functionality, and of the spatial-temporal context at aggregate-level for the relevance of plant-microbe interactions, introduce important implications involving the role of microorganisms in the rhizosphere and require an integrated analysis. Herein, the rhizosphere is a focus – a habitat of selected low-abundance species, where important microbial groups act in S turnover and plant growth – while keeping a perspective on important microbial feedback S fluxes that may occur in bulk soils., This work was supported by “Fundação para a Ciência e a Tecnologia” under FCT R&D Unit funding UIDB/00329/2020 and project LxCrop (FCT-ECF 2020/2395)

Background The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation. Results Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism. Conclusions Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha−1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p blactx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.

Improved mechanistic understanding of soil methane (CH4) exchange responses to shifts in soil moisture and temperature in forest ecosystems is pivotal to reducing uncertainty in estimates of the soil-atmospheric CH4 budget under climate change. We investigated the mechanism behind the effects of soil moisture and temperature shifts on soil CH4 fluxes under laboratory conditions. Soils from the Huai River Basin in China, an area that experiences frequent hydrological shifts, were sampled from two consecutive depths (0–20 and 20–50 cm) and incubated for 2 weeks under different combinations of soil moisture and temperature. Soils from both depths showed an increase in soil moisture and temperature-dependent cumulative CH4 fluxes. CH4 production rates incubated in different moisture and temperature in surface soil ranged from 1.27 to 2.18 ng g−1 d−1, and that of subsurface soil ranged from 1.18 to 2.34 ng g−1 d−1. The Q10 range for soil CH4 efflux rates was 1.04–1.37. For surface soils, the relative abundance and diversity of methanotrophs decreased with moisture increase when incubated at 5 °C, while it increased with moisture increase when incubated at 15 and 30 °C. For subsurface soils, the relative abundance and diversity of methanotrophs in all samples decreased with moisture increase. However, there was no significant difference in the diversity of methanogens between the two soil depths, while the relative abundance of methanogens in both depths soils increased with temperature increase when incubated at 150% water-filled pore space (WFPS). Microbial community composition exhibited large variations in post incubation samples except for one treatment based on the surface soils incubated at 15 °C, which showed a decrease in the total and unique species number of methanotrophs with moisture increase. In contrast, the unique species number of methanogens in surface soils increased with moisture increase. The analysis of distance-based redundancy analysis (db-RDA) showed that soil pH, dissolved organic carbon (DOC), dissolved organic nitrogen (DON), microbial biomass carbon (MBC), NO3−-N, and NH4+-N mainly performed a significant effect on methanotrophs community composition when incubated at 60% WFPS, while they performed a significant effect on methanogens community composition when incubated at 150% WFPS. Overall, our findings emphasized the vital function of soil hydrology in triggering CH4 efflux from subtropical plantation forest soils under future climate change.

Vegetation change of the Arctic tundra due to global warming is a well-known process, but the implication for the belowground microbial communities, key in nutrient cycling and decomposition, is poorly understood. We characterized the fungal and bacterial abundances in litter and soil layers across 16 warming experimental sites at 12 circumpolar locations. We investigated the relationship between microbial abundances and nitrogen (N) and carbon (C) isotopic signatures, indicating shifts in microbial processes with warming. Microbial abundances were 2–3 orders of magnitude larger in litter than in soil. Local, site-dependent responses of microbial abundances were variable, and no general effect of warming was detected. The only generalizable trend across sites was a dependence between the warming response ratios and C:N ratio in controls, highlighting a legacy of the vegetation on the microbial response to warming. We detected a positive effect of warming on the litter mass and δ15N, which was linked to bacterial abundance under warmed conditions. This effect was stronger in experimental sites dominated by deciduous shrubs, suggesting an altered bacterial N-cycling with increased temperatures, mediated by the vegetation, and with possible consequences on ecosystem feedbacks to climate change. Vegetation change of the Arctic tundra due to global warming is a well-known process, but the implication for the belowground microbial communities, key in nutrient cycling and decomposition, is poorly understood. We characterized the fungal and bacterial abundances in litter and soil layers across 16 warming experimental sites at 12 circumpolar locations. We investigated the relationship between microbial abundances and nitrogen (N) and carbon (C) isotopic signatures, indicating shifts in microbial processes with warming. Microbial abundances were 2–3 orders of magnitude larger in litter than in soil. Local, site-dependent responses of microbial abundances were variable, and no general effect of warming was detected. The only generalizable trend across sites was a dependence between the warming response ratios and C:N ratio in controls, highlighting a legacy of the vegetation on the microbial response to warming. We detected a positive effect of warming on the litter mass and δ15 N, which was linked to bacterial abundance under warmed condi-tions. This effect was stronger in experimental sites dominated by deciduous shrubs, sug-gesting an altered bacterial N-cycling with increased temperatures, mediated by the vegetation, and with possible consequences on ecosystem feedbacks to climate change.

To minimize negative impacts of intensive agricultural practice, organic farming has been proposed as a sustainable agricultural practice with the main principles of the ecological cycle and biodiversity. This concept heavily relies on an active soil microbial community to break down organic matter into plant available nutrients. The main objective of the study was to identify whether significant differences in microbial properties in soils under soybean organic and conventional farming management exist. The study included 95 samples of soil under certified organic soybean production and 48 samples in conventional production system. Soil samples were collected form soybean rizosphere, in the period of soybean full bloom. The abundance of the examined microbial communities was assessed by an indirect dilution spread-plating method on an appropriate nutritive media. Dehydrogenase and β-glucosidase activity were measured spectrophotometrically. The variables were analyzed using two-way analysis of variance (ANOVA), followed by mean separation according to Tukey’s test at the P

The anionic surfactant SLES (sodium lauryl ether sulfate) is an emerging contaminant, being the main component of foaming agents that are increasingly used by the tunnel construction industry. To fill the gap of knowledge about the potential SLES toxicity on plants, acute and chronic effects were assessed under controlled conditions. The acute ecotoxicological test was performed on Lepidum sativum L. (cress) and Zea mays L. (maize). Germination of both species was not affected by SLES in soil, even at concentrations (1200 mg kg−1) more than twice higher than the maximum realistic values found in contaminated debris, thus confirming the low acute SLES toxicity on terrestrial plants. The root elongation of the more sensitive species (cress) was instead reduced at the highest SLES concentration. In the chronic phytotoxicity experiment, photosynthesis of maize was downregulated, and the photosynthetic performance (PITOT) significantly reduced already under realistic exposures (360 mg kg−1), owing to the SLES ability to interfere with water and/or nutrients uptake by roots. However, such reduction was transient, likely due to the rapid biodegradation of the surfactant by the soil microbial community. Indeed, SLES amount decreased in soil more than 90% of the initial concentration in only 11 days. A significant reduction of the maximum photosynthetic capacity (Pnmax) was still evident at the end of the experiment, suggesting the persistence of negative SLES effects on plant growth and productivity. Overall results, although confirming the low phytotoxicity and high biodegradability of SLES in natural soils, highlight the importance of considering both acute and nonlethal stress effects to evaluate the environmental compatibility of soil containing SLES residues.

The effects of climate change-induced ice melting on the microbial communities in different glacial-fed aquatic systems have been reported, but seasonal dynamics remain poorly inves-tigated. In this study, the structural and functional traits of the aquatic microbial community were assessed along with the hydrological and biogeochemical variation patterns of the Arctic Pasvik River under riverine and brackish conditions at the beginning (May = Ice-melt(-)) and during the ice-melting season (July = Ice-melt(+)). The microbial abundance and morphometric analysis showed a spatial diversification between the riverine and brackish stations. Results highlighted different levels of microbial respiration and activities with different carbon and phosphorous utilization pathways, thus suggesting an active biogeochemical cycling along the river especially at the beginning of the ice-melting period. At Ice-melt(-), Gammaproteobacteria and Alphaproteobacteria were dominant in riverine and brackish stations, respectively. Conversely at Ice-melt(+), the microbial community composition was more homogeneously distributed along the river (Gammaproteobacteria>Alphaproteobacteria> Bacteroidetes). Our findings provide evidence on how riverine microbial communities adapt and respond to seasonal ice melting in glacial-fed aquatic ecosystems.

Palmitic acid (PA) in root exudates or decaying residues can reduce the incidence of soil-borne diseases and promote the growth of some crop plants. However, the effects of PA on soil-borne pathogens and microbial communities are poorly understood. Here, we investigate the effects of PA on overall watermelon microbial communities and the populations of Fusarium oxysporum f.sp. niveum (Fon). The effects of PA on the mycelial growth and spore production of Fon were tested in vitro, while its effects on Fon, total bacteria and total fungi populations, and microbial communities were evaluated in a pot experiment. The results revealed that all test concentrations of PA inhibited Fon mycelia growth and spore production. The pot experiment showed that 0.5 mM and 1 mM PA reduced Fon but increased total bacteria populations, and 0.5 mM and 1 mM PA 0.5 mM and 1 mM PA promoted the change to a soil type of bacteria soil. Meanwhile, 0.5 mM PA and 1 mM PA altered the community composition of the rhizosphere microorganisms and reduced the relative abundance of two bacterial operational taxonomic units (OTUs) and the two fungal OTUs that were significantly (p

The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P

The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities., Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates). IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.

As the microbiome is composed of a variety of microbial interactions, it is imperative in microbiome research to identify a microbial sub-community that collectively conducts a specific function. However, current methodologies have been highly limited to analyzing conditional abundance changes of individual microorganisms without considering group-wise collective microbial features. To overcome this limitation, we developed a network-based method using nonnegative matrix factorization (NMF) to identify functional meta-microbial features (MMFs) that, as a group, better discriminate specific environmental conditions of samples using microbiome data. As proof of concept, large-scale human microbiome data collected from different body sites were used to identify body site-specific MMFs by applying NMF. The statistical test for MMFs led us to identify highly discriminative MMFs on sample classes, called synergistic MMFs (SYMMFs). Finally, we constructed a SYMMF-based microbial interaction network (SYMMF-net) by integrating all of the SYMMF information. Network analysis revealed core microbial modules closely related to critical sample properties. Similar results were also found when the method was applied to various disease-associated microbiome data. The developed method interprets high-dimensional microbiome data by identifying functional microbial modules on sample properties and intuitively representing their systematic relationships via a microbial network.

Climate warming affects the carbon cycle of northern peatlands through temperature rises and a changing carbon availability. To clarify the effects of elevated temperature and labile carbon addition on SOC mineralization, as well as their microbial driving mechanisms, topsoil (0–10 cm) and subsoil (10–20 cm) were collected from a peatland in the Great Hing’an Mountains and incubated with or without 13C-glucose at 10 °C and 15 °C for 42 days. The results showed that 5 °C warming significantly stimulated SOC mineralization along with NH4+-N and NO3−-N content increases, as well as a decrease in invertase and urease activities. Glucose addition triggered a positive priming effect (PE) in the early stage of the incubation but changed to a negative PE in the late stage of the incubation. Glucose likely regulates carbon dynamics by altering fungi: bacteria, soil invertase, and β-glucodase activities, and MBC, DOC, NH4+-N contents. Glucose addition increased fungal abundance in 0–10 cm at 10 °C and 15 °C, and 10–20 cm at 10 °C, respectively, but significantly decreased fungal abundance in 10–20 cm at 15 °C. Glucose addition decreased bacterial abundance in 0–10 cm at 10 °C but increased bacterial abundance in 10–20 cm soil at 10 °C, and in 0–10 and 10–20 cm soils at 15 °C, respectively. Glucose addition significantly decreased the fungi: bacteria ratio in 0–20 cm soils at 15 °C. In addition, Q10 was significantly positively correlated with the changes in soil DOC, NH4+-N contents, invertase, and β-glucosidase activities, while negatively correlated with fungi: bacteria and urease activities after 5 °C of warming, and glucose addition significantly increased the Q10. Labile carbon may decrease carbon losses in northern peatlands that inhibit warming-induced carbon emission increase, thus partially buffering soil carbon content against change.

World population growth has led to a rise in resource demands imposed on agricultural systems, generating an increased global use of natural resources. However, agroecology proposes self-regulation in order to achieve a sustainable agricultural balance. Therefore, considering the rapid responses of microbial communities to small changes in soil use, the objective of this study was to assess the response of soil microbial communities to agroecological vs. conventional systems of extensive agriculture. Soil sampling was carried out in 2016 and 2017 with three different treatments using the sequence soybean/maize (Glycine max L./Zea mays L.) as the main crop: Agroecological (AE), conventional with cover crops (CC) and conventional without cover crops (control). Species used as cover crops were wheat (Triticum aestivum), vetch (Vicia sativa L.), oat (Avena sativa L.) and radish (Raphanus sativus L.). Agroecological treatment showed the lowest total nitrogen (0.18 mg N g−1) and organic carbon (1.99 mg C g−1) content of soil, and CC treatment showed the highest value of fluorescein diacetate hydrolysis, with values 63.2% and 12.1% higher than AE and the control, respectively. However, AE treatment also produced the highest F:B ratio (44.8) and the lowest metabolic quotient (1.14), which indicates an improvement in metabolic efficiency and soil quality. No significant differences were recorded in the abundance of fungal and bacterial communities between treatments. Our results suggest that agroecological management is characterised by fungal dominance in soil microbial communities and a higher microbial metabolic efficiency compared to conventional management. These results demonstrate more efficient use of carbon substrates in agroecological systems, which could counteract the negative effect of the lack of synthetic fertilisation and reduced-tillage in the long term. The findings demonstrate that sustainable agricultural tools with adequate management can be effectively used to preserve soil quality. Fil: Chavarría, Diego Nicolás. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Perez Brandan, Carolina Gabriela. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Salta-Jujuy. Estación Experimental Agropecuaria Salta; Argentina Fil: Serri, Dannae. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina Fil: Meriles, Jose Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Ciencia y Tecnología de Alimentos Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Ciencia y Tecnología de Alimentos Córdoba; Argentina Fil: Restovich, Silvina Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; Argentina Fil: Andriulo, Adrian Enrique. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; Argentina Fil: Jacquelin, Luis. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria Pergamino; Argentina Fil: Vargas Gil, Silvina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities., High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards. IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

Cover cropping is a promising sustainable agricultural method with the potential to enhance soil health and mitigate consequences of soil degradation. Because cover cropping can form an agroecosystem distinct from that of bare fallow, the soil microbiome is hypothesized to respond to the altered environmental circumstances. Despite the growing number of primary literature sources investigating the relationship between cover cropping and the soil microbiome, there has not been a quantitative research synthesis that is sufficiently comprehensive and specific to this relationship. We conducted a meta-analysis by compiling the results of 60 relevant studies reporting cover cropping effects on soil microbial properties to estimate global effect sizes and explore the current landscape of this topic. Overall, cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Moreover, cover cropping effect sizes varied by agricultural covariates like cover crop termination or tillage methods. Notably, cover cropping effects were less pronounced under conditions like continental climate, chemical cover crop termination, and conservation tillage. This meta-analysis showed that the soil microbiome can become more robust under cover cropping when properly managed with other agricultural practices. However, more primary research is still needed to control between-study heterogeneity and to more elaborately assess the relationships between cover cropping and the soil microbiome. Fil: Kim, Nakian. University of Illinois at Urbana; Estados Unidos Fil: Zabaloy, Maria Celina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina Fil: Guan, Kaiyu. University of Illinois at Urbana; Estados Unidos Fil: Villamil, Maria Bonita. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Illinois at Urbana; Estados Unidos

Increased concerns associated with interactions between herbicides, inorganic fertilizers, soil nutrient availability, and plant phytotoxicity in perennial tree crop production systems have renewed interest in the use of cover crops in the inter-row middles or between trees as an alternative sustainable management strategy for these systems. Although interactions between the soil microbiome and cover crops have been examined for annual cropping systems, there are critical differences in management and growth in perennial cropping systems that can influence the soil microbiome and, therefore, the response to cover crops. Here, we discuss the importance of cover crops in tree cropping systems using multispecies cover crop mixtures and minimum tillage and no-tillage to not only enhance the soil microbiome but also carbon, nitrogen, and phosphorus cycling compared to monocropping, conventional tillage, and inorganic fertilization. We also identify potentially important taxa and research gaps that need to be addressed to facilitate assessments of the relationships between cover crops, soil microbes, and the health of tree crops. Additional evaluations of the interactions between the soil microbiome, cover crops, nutrient cycling, and tree performance will allow for more effective and sustainable management of perennial cropping systems.

Surface mining activities, despite their benefits, lead to the deterioration of local and regional environmental quality and play a role in global ecosystem pollution. This research aimed to estimate the culturable microbial population structure at five locations near the opencast coal mine "Kakanj" (Bosnia and Herzegovina) via agar plate and phospholipid fatty acids (PLFA) method and to establish its relationship to the physical and chemical properties of soil. Using the ICP-OES method, the heavy metal pollution of all examined locations (overburden, former grass yard, forest, arable soil, and greenhouse) was observed. Substantial variations among the sites regarding the most expressed indicators of heavy metal pollution were noted; Cr, Pb, Ni, and Cu content ranged from 63.17 to 524.47, 20.57 to 349.47, 139.13 to 2785.67, and 25.97 to 458.73 mg/kg, respectively. In the overburden sample, considerable low microbial activity was detected; the bacterial count was approximately 6- to 18-fold lower in comparison with the other samples. PLFA analysis showed the reduction of microbial diversity, reflected through the prevalence of normal and branched saturated fatty acids, their ratio (ranged from 0.92 to 7.13), and the absence of fungal marker 18:2 omega 6 fatty acid. The principal component analysis showed a strong negative impact of heavy metals Na and B on main microbial and PLFA profiles. In contrast, stock of main chemical parameters, including Ca, K, Fe, and pH, was positively correlated with the microbial community structure.

Permafrost, permanently frozen soil, constitutes a major portion of the Earth’s terrestrial cryosphere and represents a unique niche for cold-adapted microorganisms. As the global temperature increases, it is still unknown what consequences this will have for the inhabiting microbial structure and diversity. We assessed the microbial diversity within permafrost in Adventdalen, Svalbard across two different years (2016 and 2019). Our results revealed that the living conditions of the indigenous microorganisms had changed, due to an increase in moisture and organic matter. Furthermore, we observed that the bacterial and fungal gene abundance had also increased. The majority of the microorganisms discovered within our samples are recognised as degraders of complex carbon compounds, indicating that a potential increase of carbon dioxide emissions is likely to be a consequence of the further increase in global temperatures. Due to differing study design across years, exact replicates were not possible, and most of the measured data would not be statistically reliable if compared directly to each other. However, one depth from each of the cores could be directly compared, and here we observed an overall increase in moisture content, organic matter, and in microbial abundance. We thus infer that there is a possibility of increased greenhouse gas release when the microbial living conditions have shifted. Masteroppgave i biologi BIO399 MAMN-BIO

Soil microorganisms are an important component of soil health and drive key biogeochemical processes. The objective was to assess the impacts of fall cover crops (CC), main crops (MC) and residue harvest on the abundance, diversity and function of bacteria and fungi over the growing season. A medium-term trial was established in a horticultural rotation with annual fall CCs. Microbial communities after winter wheat and tomatoes were examined. After MC harvest, CC treatments (none, oat, radish, rye, rye/radish mixture) were applied and plots were split for MC residue retention. Microbial abundances were quantified throughout the growing season with qPCR and sequenced annually with Illumina MiSeq. CCs significantly increased bacterial (rye, radish/rye) and fungal (radish, radish/rye) abundance compared to the no-cover control. PiCRUST and FUNGuild analysis found that bacterial and fungal diversity and functions were significantly impacted by MC species as well as increased by the inclusion of rye and radish. Ontario Ministry of Agriculture, Food and Rural Affairs

Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha−1. Soil samples were collected at a 0–15 cm depth from 2016–2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P P

The effects of climate change-induced ice melting on the microbial communities in different glacial-fed aquatic systems have been reported, but seasonal dynamics remain poorly investigated. In this study, the structural and functional traits of the aquatic microbial community were assessed along with the hydrological and biogeochemical variation patterns of the Arctic Pasvik River under riverine and brackish conditions at the beginning (May = Ice-melt (−)) and during the ice-melting season (July = Ice-melt (+)). The microbial abundance and morphometric analysis showed a spatial diversification between the riverine and brackish stations. Results highlighted different levels of microbial respiration and activities with different carbon and phosphorous utilization pathways, thus suggesting an active biogeochemical cycling along the river especially at the beginning of the ice-melting period. At Ice-melt (−), Gammaproteobacteria and Alphaproteobacteria were dominant in riverine and brackish stations, respectively. Conversely, at Ice-melt (+), the microbial community composition was more homogeneously distributed along the river (Gammaproteobacteria &gt, Alphaproteobacteria &gt, Bacteroidetes). Our findings provide evidence on how riverine microbial communities adapt and respond to seasonal ice melting in glacial-fed aquatic ecosystems.

Assessing the impacts of land use on soil respiration (Rs) and its temperature sensitivity (Q10) is of vital significance for understanding regional carbon cycles. In this study, the regulation of Rs and Q10 by soil biotic and abiotic factors under different land-use types, i.e., cropland, apple orchard, abandoned land, Coronilla varia grassland, and Robinia pseudoacacia woodland, were examined in the Luoyugou watershed on the Chinese Loess Plateau. We monitored Rs, soil temperature, and moisture in situ from July to December 2018 and evaluated soil microbial abundance, root biomass, carbon and nitrogen nutrient levels. The results showed that soil organic carbon, total nitrogen, available nitrogen, dissolved organic carbon, and microbial biomass carbon decreased by the following order: grassland > woodland > abandoned land > cropland > orchard. The high amounts of plant residues and the low levels of human disturbance in grassland and woodland contributed to higher soil carbon and nitrogen nutrient levels in these land-use types than in cropland and orchard. Rs decreased from July to December, with soil temperature and moisture being the key explanatory factors. The mean Rs in grassland (3.68 μmol m−2 s−1) and woodland (3.81 μmol m−2 s−1) was significantly higher than that in cropland, orchard, and abandoned land. Q10 ranged from 1.77 to 5.87 across all land-use types, and orchard, abandoned land, grassland, and woodland had Q10 values 1.91, 1.37, 1.47, and 3.32 times higher, respectively, than the Q10 of cropland. The variable importance in the projection (VIP) values from the partial least squares regression model showed that soil temperature (VIP = 1.41), pH (VIP = 1.22), microbial biomass nitrogen (VIP = 1.13), microbial biomass carbon (VIP = 1.12), bacterial abundance (VIP = 1.12), available nitrogen (VIP = 1.01), and soil moisture (VIP = 1.01) were the most important predictors of Rs. Our study suggests that soil temperature and labile organic matter exert stronger impacts on Rs than do microbial abundance and root biomass. Our results contribute to a better understanding of ecosystem carbon cycles.

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

The importance of soil microbial flora in agro-ecosystems is well known, but there is limited understanding of the effects of long-term fertilization on soil microbial community succession in different farming management practices. Here, we report the responses of soil microbial community structure, abundance and activity to chemical (CF) and organic fertilization (OF) treatments in a sandy agricultural system of wheat-maize rotation over a 17-year period. Illumina MiSeq sequencing showed that the microbial community diversity and richness showed no significant changes in bacteria but decreased in fungi under both CF and OF treatments. The dominant species showing significant differences between fertilization regimes were Actinobacteria, Acidobacteria and Ascomycota at the phylum level, as well as some unclassified genera of other phyla at the genus level. As expected, soil organic matter content, nutrient element concentrations and bacterial abundance were enhanced by both types of fertilization, especially in OF, but fungal abundance was inhibited by OF. Redundancy analysis revealed that soil enzyme activities were closely related to both bacterial and fungal communities, and the soil nutrient, texture and pH value together determined the community structures. Bacterial abundance might be the primary driver of crop yield, and soil enzyme activities may reflect crop yield. Our results suggest a relatively permanent response of soil microbial communities to the long-term fertilization regimes in a reclaimed sandy agro-ecosystem from a mobile dune, and indicate that the appropriate dosage of chemical fertilizers is beneficial to sandy soil sustainability.

Istraživanje je obuhvatilo utvrđivanje brojnosti pojedinih sistematskih i fizioloških grupa mikroorganizama, kao i određivanje aktivnosti enzima dehidrogenaze u zemljištima vinograda. Mikrobiološke karakteristike zavisile su od fizičkih i hemijskih osobina zemljišta na pojedinim parcelama. Najpovoljniji uslovi za razvoj i aktivnost mikroorganizama karakterisali su zemljišta neutralne i slabo alkalne reakcije, dok je najmanja brojnost većine mikroorganizama i enzimatska aktivnost zabeležena u kiselim zemljištima. Prisustvo lakopristupačnog bakra iznad 50 mg/kg zabeleženo je samo u 4% ispitivanih zemljišta, stoga dobijeni rezultati ne mogu potvrditi uticaj bakra na mikrobiološke karakteristike. The study included the determination of the abundance of specific systematic and physiological groups of microorganisms, as well as the determination of the activity of the enzyme dehydrogenase in vineyard soils. Microbiological characteristics depended on the physical and chemical properties of the soil in individual plots. The most favorable conditions for the development and activity of microorganisms were characterized by soils of neutral and slightly alkaline reactions, while the lowest abundance of most microorganisms and enzymatic activity was recorded in acidic soils. The presence of readily available copper above 50 mg / kg was recorded in only 4% of the tested soils, therefore the results obtained cannot confirm the influence of copper on microbial characteristics.

Cropland soil respiration (Rs) is a major part of CO2 transportation between the atmosphere and terrestrial ecosystems. Stalk retention is an effective method to conduct sustainable agricultural development. However, the relationship between long-term maize (Zea mays L.) stalk retention and seedtime Rs is not yet fully understood; two experimental zones with the same management history were therefore chosen to conduct the comparative study. Rainfed maize monoculture was the only crop cultivated in the study site. One zone (CZ) was covered by 5639 kg ha-1 maize stalk residue (MSR) after harvesting, and the other zone (BZ) has been left bare since autumn 2000. Annual measurements with 10 replicates were conducted at seedtime in 2015, 2016, and 2017. Results showed that mean Rs was 4.11 and 4.99 (g CO2 g-1 soil h-1 for CZ and BZ, respectively. Compared with BZ, CZ soil moisture was higher, but its soil temperature was lower. Although soil microbial abundances in CZ and BZ had decreasing trends between two adjacent seedtimes, there was a nonsignificant decrease of actinomycetes (p > 0.1) and fungi (p > 0.1) in BZ. The mean percentages of alkyl-carbon (Alkyl-C) were 25.6% and 35.0% for CZ and BZ, respectively. Redundancy analyses (RDA) showed that decreasing soil temperature, soil fungi, Alkyl-C as well as increasing soil moisture could explain reduced Rs in CZ. Maize stalk retention reduces seedtime Rs, thus maize stalk retention might contribute to soil C sequestration.

Surface ice and cryoconite holes of two types of polythermal Svalbard Glaciers (Hans Glacier—grounded tidewater glacier and Werenskiold Glacier—land-based valley glacier) were investigated in terms of chemical composition, microbial abundance and diversity. Gathered data served to describe supraglacial habitats and to compare microbe–environment interactions on those different type glaciers. Hans Glacier samples displayed elevated nutrient levels (DOC, nitrogen and seston) compared to Werenskiold Glacier. Adjacent tundra formations, bird nesting sites and marine aerosol were candidates for allochtonic enrichment sources. Microbial numbers were comparable on both glaciers, with surface ice containing cells in the range of 104 mL−1 and cryoconite sediment 108 g−1 dry weight. Denaturating gradient gel electrophoresis band-based clustering revealed differences between glaciers in terms of dominant bacterial taxa structure. Microbial community on Werenskiold Glacier benefited from the snow-released substances. On Hans Glacier, this effect was not as pronounced, affecting mainly the photoautotrophs. Over-fertilization of Hans Glacier surface was proposed as the major factor, desensitizing the microbial community to the snow melt event. Nitrogen emerged as a limiting factor in surface ice habitats, especially to Eukaryotic algae. Electronic supplementary material The online version of this article (doi:10.1007/s00792-015-0764-z) contains supplementary material, which is available to authorized users.

Sponge species have been deemed high microbial abundance (HMA) or low microbial abundance (LMA) based on the composition and abundance of their microbial symbionts. In the present study, we evaluated the richness and composition of bacterial communities associated with one HMA sponge (Xestospongia testudinaria; Demospongiae: Haplosclerida: Petrosiidae), one LMA sponge (Stylissa carteri; Demospongiae: Scopalinida - Scopalinidae), and one sponge with a hitherto unknown microbial community (Aaptos suberitoides; Demospongiae: Suberitida: Suberitidae) inhabiting the Misool coral reef system in the West Papua province of Indonesia. The bacterial communities of these sponge species were also compared with seawater and sediment bacterial communities from the same coastal coral reef habitat. Using a 16S rRNA gene barcoded pyrosequencing approach, we showed that the most abundant phylum overall was Proteobacteria. The biotope (sponge species, sediment or seawater) explained almost 84% of the variation in bacterial composition with highly significant differences in composition among biotopes and a clear separation between bacterial communities from seawater and S. carteri; X. testudinaria and A. suberitoides and sediment. The Chloroflexi classes SAR202 and Anaerolineae were most abundant in A. suberitoides and X. testudinaria and both of these species shared several OTUs that were largely absent in the remaining biotopes. This suggests that A. suberitoides is a HMA sponge. Although similar, the bacterial communities of S. carteri and seawater were compositionally distinct. These results confirm compositional differences between sponge and non-sponge biotopes and between HMA and LMA sponges. published

The 9th International Workshop on Sand - Dust storm and Associated Dustfall (DUSTWORKSHOP9), 22-24 May 2018, Tenerife, Spain.-- 2 pages, Airborne particles comprise not only mineral dust but also a significant fraction of microbes and biogenic particles. Surveys of microbial diversity conducted in the last decades across all kinds of marine and terrestrial ecosystems have uncovered a striking diversity of microbial life. Yet, the abundance and composition of airborne microbial assemblages have received little attention as compared to terrestrial and marine environments. The few studies available focus mostly on continental or coastal air masses, while the organisms suspended in the atmosphere over the open oceans, which cover most of the Earth’s surface, remain unexplored. This study presents the first global survey of airborne microbes conducted over the Atlantic, Indian and Pacific Oceans during the Malaspina Circumnavigation Expedition. Thousands of taxonomically different microbes were found, uncovering a large diversity of airborne microbes comparable to that of terrestrial and marine environments. Our results show a large contribution of marine organisms to the total found in the global atmosphere, but also that terrestrial contributions make a large fraction of the airborne microorganisms found at remote marine locations. We estimate that atmospheric circulation may transfer microbes as fast as thousands of kilometers per day, sufficient to allow for intercontinental transport of microbes, This is a contribution to the Malaspina Expedition 2010, funded by the INGENIO 2010 CONSOLIDER program (ref. CDS2008-00077) of the Spanish Ministry of Economy and Competitiveness

Two pockets of liquid hypersaline brines, separated by a layer of ice with a thickness of 12 cm, were sampled from the unexplored Antarctic perennially frozen lake Tarn Flat at two depths (3.90 and 4.50 m) characterized by different salinity and pH values. Prokaryotic cell abundance and phenotypic traits were quantified by Image Analysis; prokaryotes, high and low nucleic acid content cells and virus-like particle abundances were quantified by flow cytometry; the biodiversity indices of the microbial assemblage were assessed by Biolog ecoplates. The potential rates of ectoenzymatic activities (Leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) were assessed by fluorimetry.

The perennial ice cover of Antarctic lakes sometimes encapsulate lenses of brines. In October-November 2014, a screening of several frozen lakes in the Northern Victoria Land through the ground probing radar investigation was made. Tewo lenses of liquid brines were found at different depths in two adjacent frozen Boulder Clay lakes and had a different salinity and pH. Brines were sampled under sterile conditions and analysed by microscopic image analysis to assess prokaryotic abundance, cell shape and respiring cells and by flow cytometry to determine virus abundance. The physiological profiles by Biolog ecoplate were determined as well as the potential ectoenzymatic activities rates (leucine aminopeptidase, beta-glucosidae and alkaline phosphatase).

International audience; •Aquaponics could tolerate a wide range of pH from 6.0 to 9.0.•Higher nitrogen utilization efficiency and N2O emission were achieved at pH 6.0.•Denitrification accounted for 75.2–78.5% of N2O emission from aquaponics.•Unfavorable conditions for denitrifiers led to higher N2O emission at pH 6.0. To investigate the effects of pH on performance and nitrogen transformations in aquaponics, media-based aquaponics operated at pH 6.0, 7.5 and 9.0 were systematically examined and compared in this study. Results showed that nitrogen utilization efficiency (NUE) reached its maximum of 50.9% at pH 6.0, followed by 47.3% at pH 7.5 and 44.7% at pH 9.0. Concentrations of nitrogen compounds (i.e., TAN, NO2−-N and NO3−-N) in three pH systems were all under tolerable levels. pH had significant effect on N2O emission and N2O conversion ratio decreased from 2.0% to 0.6% when pH increased from 6.0 to 9.0, mainly because acid environment would inhibit denitrifiers and lead to higher N2O emission. 75.2–78.5% of N2O emission from aquaponics was attributed to denitrification. In general, aquaponics was suggested to maintain pH at 6.0 for high NUE, and further investigations on N2O mitigation strategy are needed.

Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated different approaches (washing, sonication, and bleaching) regarding their efficiency to separate microbial cells associated with different root compartments of soil-grown rice using fluorescence microscopy and community fingerprinting of 16S rRNA genes. Vigorous washing detached 45% of the rhizoplane population compared to untreated roots. Additional sonication reduced rhizoplane-attached microorganisms by up to 78% but caused various degrees of root tissue destruction at all sonication intensities tested. Treatment with sodium hypochlorite almost completely (98%) removed rhizoplane-associated microbial cells. Community fingerprinting revealed that microbial communities obtained from untreated, washed, and sonicated roots were not statistically distinguishable. Hypochlorite-treated roots harbored communities significantly different from all other samples, likely representing true endospheric populations. Applying these procedures to other root samples (bean and clover) revealed that treatment efficiencies were strongly affected by root morphological parameters such as root hair density and rigidity of epidermis. Our findings suggest that a careful evaluation of separation strategies prior to molecular community analysis is indispensable, especially when endophytes are the subject of interest.

Aims: To determine the relationship between microbial abundance and enzyme activities of rhizosphere soil from different resistant eggplant cultivars and resistance of eggplant to Verticillium wilt. Study Design: The changes of microbial and enzymatic activities of the rhizosphere soil from different resistant eggplants after inoculation of Verticillium dahliae were analysed. Place and Duration of Study: The plants were grown in a plastic greenhouse of the Vegetable Crops Experimental Station, and the laboratory experiments were conducted at the Horticulture College, Shenyang Agricultural University from August to November, 2008. Methodology: 14 eggplant cultivars were selected and inoculated with Verticillium dahliae to screen their resistance against Verticillium wilt, and classified according the final disease index. The quantities of main cultivable microorganisms and some functional bacteria were investigated by the serial dilution method. Activities of oxidoreductase and hydrolase enzymes of rhizosphere soil were determined by spectrophotometry or colorimetric titrations. Results: The correlation analysis among resistance of eggplant to Verticillium wilt, microorganisms and enzyme activities showed that, the abundance of actinomyces, the ratios of bacteria to fungi and actinomyces to fungi, and the activities of catalase, polyphenol oxidase, protease and urease, were significantly positively related with the resistance.

This study investigated the effects of disodium fumarate (DF) on methane emission, ruminal fermentation and microbial abundance in goats under different forage (F) : concentrate (C) ratios and fed according to maintenance requirements. Four ruminally fistulated, castrated male goats were used in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and the main factors being the F : C ratios (41 : 59 or 58 : 42) and DF supplementation (0 or 10 g/day). DF reduced methane production (P < 0.05) on average by 11.9%, irrespective of the F : C ratio. The concentrations of total volatile fatty acids, acetate and propionate were greater in the rumen of goats supplemented with DF (P < 0.05), whereas the abundance of methanogens was lower (P < 0.05). In high-forage diets, the abundance of Selenomonas ruminantium, a fumarate-reducing bacterium, was greater in the rumen of goats supplemented with DF. The abundance of fungi, protozoa, Ruminococus flavefaciens and Fibrobacter succinogenes were not affected by the addition of DF. Variable F : C ratios affected the abundance of methanogens, fungi and R. flavefaciens (P < 0.05), but did not affect methane emission. The result implied that DF had a beneficial effect on the in vivo rumen fermentation of the goats fed diets with different F : C ratios and that this effect were not a direct action on anaerobic fungi, protozoa and fibrolytic bacteria, the generally recognized fiber-degrading and hydrogen-producing microorganisms, but due to the stimulation of fumarate-reducing bacteria and the depression of methanogens.