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Aims: Application of cattle manure could improve soil fertility by increasing the stability of soil organic carbon (SOC), however, the extent of this effect might depend on the soil layer. This study aims at evaluating the differences in SOC chemistry between topsoil and subsoil caused by cattle manure addition. Methods: Here, a 90-day pot experiment was used to investigate the SOC chemical structure (13C-NMR and FTIR), as well as microbial community composition (PLFA), with cattle manure amended in topsoil (T1M) and subsoil (T2M) and without manure in topsoil (T1) and subsoil (T2). Results: Application of cattle manure significantly increased SOC, total nitrogen (TN) contents and plant biomass either in topsoil or subsoil. The alkyl C/O-alkyl C (A/OA) ratio of T1M was lower than that of T1, while T2M was greater than that of T2, indicating the SOC of T1M decomposition was delayed but of T2M was promoted. The A/OA ratio of T2M was greater than that of T1M, indicating the decomposition degree of SOC of T2M was greater. The fungi/bacterial PLFA ratio, G+/G− PLFA ratio and fungi PLFA were lower in T2M than T1M. RDA analysis demonstrated that O-alkyl C was negatively associated with bacterial and G- PLFA, especially Gemmatimonadetes and Acidobacteria, while positive correlation with fungi PLFA. However, the alkyl C was negatively associated with fungi PLFA, especially Basidiomycota. Conclusions: The subsoil with cattle manure added promoted bacterial consumed labile C, especially Gemmatimonadetes and Acidobacteria. Therefore, the subsoil with cattle manure added had a higher decomposition degree of SOC when compared with the topsoil with cattle manure added, improving the stability of SOC. [ABSTRACT FROM AUTHOR]

In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro‐ and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust–soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses (13CO2 and 15N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral‐associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems. [ABSTRACT FROM AUTHOR]

Cropland acidification seriously restricts sustainable agricultural development. The main purpose of this study was to determine whether deeper tilling could alleviate topsoil acidification to improve the quality of arable land. A soil column incubation experiment simulating tillage depths (10 cm, 30 cm and 50 cm) and lime addition was conducted to determine their effects on soil acidification improvement. The changes in soil pH, exchangeable acidity, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), available phosphorus (AP), and microbial phospholipid fatty acids (PLFA) were analyzed. Tillage depth, lime application, and their interaction all had significant impacts on soil pH. T50 (simulated tillage depth of 50 cm) and T50+Lime (simulated tillage depth of 50 cm plus lime) treatments significantly increased the topsoil pH from 5.41 to 6.35 and 7.12, respectively. T50 treatment significantly reduced the soil exchangeable acid content compared to the T10 treatment. The nutrient accumulation along soil column indicated that the T50 and T50+Lime treatments significantly increased NO3−-N and AP content in the >30–50 cm soil layer. Compared with T30, NO3−-N accumulation in the >30–50 cm soil layers of T50 and T50+Lime treatments was 6.62 and 7.93 times higher, respectively. The accumulation of AP in the >30–50 cm soil layers of the T50 and T50+Lime treatments was 1.33 and 1.54 times higher than in the T30 treatment, respectively. These findings imply tillage up to 50 cm without exogenous materials could be a potential measure to reduce topsoil acidification and increase nutrition availability of >30–50 cm soil layers. Tillage of up to 30 cm combined with lime application confers greater benefits, which would particularly impact crops with shallow root systems. Subsequent field experiments will be conducted to further investigate the efficacy of these strategies in enhancing crop yield. [ABSTRACT FROM AUTHOR]

Rock fragments (RFs) are abundant soil constituents, but are routinely excluded from soil analyses. Hence, their contribution to soil properties, and in particular to the microbiome, is incompletely understood. Therefore, shifts in microbial colonisation along the rock‐to‐soil continuum of topsoils from three agricultural sites with different sedimentary parent rock materials were investigated with particular attention to RFs. Microbial biomass and community composition were quantified using phospholipid fatty acid (PLFA) analysis for unweathered and weathered parent rock materials, two RF fractions (8–16 mm and 2–8 mm) and the fine earth (FE; <2 mm). Trends in biogeochemical weathering, nutrient availability and soil organic matter (OM) development were assessed using mineralogical, geochemical and physical analyses. Actinobacterial PLFA was particularly abundant in parent rocks, where Actinobacteria likely contribute to rock weathering and the initiation of OM accumulation. Conversely, bacterial PLFAs were most abundant in the FE under nutrient‐ and OM‐rich conditions. The integral role of RFs as a microbial habitat is demonstrated by a distinct fungal colonisation, which is enabled by the specific physical features of RFs in combination with the provision of inorganic nutrients. Our findings indicate that RFs are colonised by microbes and that differences in the community structure depend on mineralogical properties and chemical weathering status. We document that RFs are microhabitats with a significant potential to host microbial life in cultivated soils, and thus, could play an important role in biogeochemical cycling and the provision of soil functions in agroecosystems. [ABSTRACT FROM AUTHOR]

Conventional agricultural practices severely deplete the soil of essential organic matter and nutrients, increasing its vulnerability to disease, drought, and flooding. Permaculture is a form of agroecology adopting a whole ecosystem approach to create a set of principles and design frameworks for enriching soil fertility, but there is little scientific evidence of its efficiency. This study compares two permaculture managed sites with a conventional arable site to investigate the effect of permaculture management on soil fertility. We used phospholipid fatty acid analysis to estimate microbial abundance and diversity and related these to measured soil nutrients and carbon stocks. The potential of permaculture management to mitigate soil greenhouse gas emissions was assessed during a laboratory soil incubation and measurement of greenhouse gases via gas chromatography. Overall, the permaculture managed allotments had three times higher microbial biomass, one and a half times higher nitrogen, and four times higher carbon content than the arable site. Permaculture soils had larger carbon dioxide and nitrous oxide fluxes compared to arable soil, but all sites had a mean negative flux in methane. Permaculture management by use of organic amendments and no-dig practices provides a constant slow release of nutrients and build-up of organic matter and carbon and consequently promotes greater bacterial and fungal biomass within the soil. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) is essential in semi-arid agricultural land for enhancing soil health, particularly through the promotion of microbial activities. This study assessed the impact of different agronomic practices on soil properties, microbial communities, and SOC levels in semi-arid Moroccan wheat fields. Three treatments were investigated: eucalyptus (Eucalyptus spp.) companion planting (EU), and fallowing with harvest residue mulching (FA), with the latter involving both short (3 months; FAS) and long (15 months; FAL) fallow periods. The study revealed significant variation in soil characteristics and microbial communities between these agronomic management regimes. Notably, soils managed with FAL contained elevated SOC levels (1.2%) compared to other treatments (FAS and EU) which show lower SOC range (0.62-0.86%). Both labile C (water-soluble carbon) and recalcitrant C (humic substances) were increased by FAL. Additionally, soil microbial biomass and dehydrogenase activity were observed to be high in FAL-managed soils, along with increased levels of extracellular enzymes related to nutrient cycling (b-glucosidase, alkaline phosphatase, and urease). Phospholipid fatty acid (PLFA) analysis indicated positive correlation between carbon content in soils and microbial populations. In contrast, soils managed with EU had significantly lower SOC levels, possibly due to differences in carbon fractionation. FAL increased soil enzymatic activities and enriched the microbial community when compared to EU management. In conclusion, this study indicated the importance of fallowing and fallowing period for conservation of SOC, and potential to mitigate negative effects of biophysical constraints on agricultural productivity in semi-arid soils of Northwest Africa. [ABSTRACT FROM AUTHOR]

Summary: The link between above‐ and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle.In young beech model ecosystems and mature naturally dry pine forest exposed to 15‐yr‐long irrigation, we performed 13C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities.The 13C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The 13C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (−85%) than by gram‐positive (−43%) and gram‐negative bacteria (−58%).13C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, 13C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest.Belowground C allocation and rhizosphere communities are highly resilient to drought. [ABSTRACT FROM AUTHOR]

The effects of intensive and reduced tillage, fertilization, and irrigation on soil chemical and microbiological parameters were studied in a long-term field experiment in Hungary. The treatments were plowing tillage, ripper tillage, strip tillage; control (without fertilization), NPK fertilization (N: 160 kg/ha; P: 26 kg/ha; K: 74 kg/ha); and non-irrigation and irrigation. Soil samples were collected through maize monoculture in the fall of 2021 in the 30th year of the experiment. The soil organic carbon, total nitrogen, soil microbial biomass (based on PLFA analysis), and soil enzyme activity were observed to be significantly high in the strip tillage plots, but were lower in the ripper tillage plots, and even lower in the plowing tillage plots. The fungal, arbuscular mycorrhiza fungal, and bacterial biomasses were significantly higher in the strip tillage and ripper tillage plots compared to the plowing tillage plots. The strip tillage treatment was found to be the most favorable cultivation method for improving the microbial biomass and activity of Chernozem soil, followed by the ripper tillage and plowing tillage treatments. The long-term use of chemical fertilizers greatly reduced the soil microbial biomass and negatively impacted the soil microbial community, leading to a decrease in fungi and Gram-negative bacteria. The ratio of cyclopropyl PLFA precursors to cyclopropyl PLFAs, as a "stress factor", indicated the most stressful bacterial environment was that found in the fertilized, non-irrigated plowed soil. [ABSTRACT FROM AUTHOR]

In recent years, the Sanjiang Plain has experienced drastic human activities, which have dramatically changed its ecological environment. Soil microorganisms can sensitively respond to changes in soil quality as well as ecosystem function. In this study, we investigated the changes in soil microbial community diversity and composition of three typical land use types (forest, wetland and cropland) in the Sanjiang Plain using phospholipid fatty acid analysis (PLFA) technology, and 114 different PLFA compounds were identified. The results showed that the soil physicochemical properties changed significantly (p < 0.05) among the different land use types; the microbial diversity and abundance in cropland soil were lower than those of the other two land use types. Soil pH, soil water content, total organic carbon and available nitrogen were the main soil physico-chemical properties driving the composition of the soil microbial community. Our results indicate that the soil microbial community response to the three different habitats is complex, and provide ideas for the mechanism by which land use changes in the Sanjiang Plain affect the structure of soil microbial communities, as well as a theoretical basis for the future management and sustainable use of the Sanjiang plain, in the northeast of China. [ABSTRACT FROM AUTHOR]

Cropland acidification seriously restricts sustainable agricultural development. The main purpose of this study was to determine whether deeper tilling could alleviate topsoil acidification to improve the quality of arable land. A soil column incubation experiment simulating tillage depths (10 cm, 30 cm and 50 cm) and lime addition was conducted to determine their effects on soil acidification improvement. The changes in soil pH, exchangeable acidity, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3−-N), available phosphorus (AP), and microbial phospholipid fatty acids (PLFA) were analyzed. Tillage depth, lime application, and their interaction all had significant impacts on soil pH. T50 (simulated tillage depth of 50 cm) and T50+Lime (simulated tillage depth of 50 cm plus lime) treatments significantly increased the topsoil pH from 5.41 to 6.35 and 7.12, respectively. T50 treatment significantly reduced the soil exchangeable acid content compared to the T10 treatment. The nutrient accumulation along soil column indicated that the T50 and T50+Lime treatments significantly increased NO3−-N and AP content in the >30–50 cm soil layer. Compared with T30, NO3−-N accumulation in the >30–50 cm soil layers of T50 and T50+Lime treatments was 6.62 and 7.93 times higher, respectively. The accumulation of AP in the >30–50 cm soil layers of the T50 and T50+Lime treatments was 1.33 and 1.54 times higher than in the T30 treatment, respectively. These findings imply tillage up to 50 cm without exogenous materials could be a potential measure to reduce topsoil acidification and increase nutrition availability of >30–50 cm soil layers. Tillage of up to 30 cm combined with lime application confers greater benefits, which would particularly impact crops with shallow root systems. Subsequent field experiments will be conducted to further investigate the efficacy of these strategies in enhancing crop yield.

The composition of a soil microbial community that is associated with novel rotation crops could contribute to an increased yield of subsequent crops and is an important factor influencing the composition of the rhizosphere microbiome. However, the effect of alternative dryland crops on soil microbial community composition is not clear in the northern Great Plains (NGP). The objective of this study, therefore, was to evaluate the effects of the oilseed crops Ethiopian mustard (Brassica carinata A.) or camelina (Camelina sativa L.) or a 10-species forage/cover crop (CC) mix and fallow on soil biological health. Phospholipid fatty acid (PLFA) analysis was used to characterize the microbial community structure. The results showed that the total bacterial PLFA proportion was significantly higher in camelina and fallow compared to CCs and carinata, whereas the total fungal proportion was significantly higher under a CC mix compared to camelina and fallow. The fungal-to-bacterial ratio was significantly higher in CCs (0.130) and carinata (0.113) compared to fallow (0.088). Fungi are often considered a good indicator of soil health, while bacteria are crucial in soil functions. The changes in specific microbial communities due to crop-related alterations might play a key role in the yield of subsequent crops. This study provides valuable insights into the effect of oilseeds, CCs, and fallow on microbial communities. [ABSTRACT FROM AUTHOR]

Background: The microbial community structure in forest soils is expected to change in response to global environmental change, such as climate warming and nitrogen deposition. Community responses to these environmental changes may further interact with the site's land-use history and understory light availability. Uncovering the relative importance of these global change drivers is crucial to understand and predict soil microbial communities' changes. Methods: A full-factorial in situ mesocosm experiment was conducted and the soil microbiota were analyzed by phospholipid fatty acid and neutral lipid fatty acid. The soils in the mesocosms were sampled from forests with different land-use history, and mesocosms contained typical forest understory plants. The mesocosms were exposed to experimental treatments of warming, nitrogen addition and subcanopy illumination. Results: Among the treatments, past land-use had the strongest effect shaping the microbial community structure. We found a significantly higher abundance of arbuscular mycorrhizal fungi and Actinobacteria in ancient forests. The soil microbial and plant communities were co-structured in ancient forests, but not in past-agricultural forests. Warming and nitrogen fertilization did not affect the soil microbial community composition, yet illumination resulted in slight changes in soil microbial composition. Conclusions: Our results underpin the role of land-use legacies in shaping soil microbial communities. The stronger plant-microbe linkages in ancient forest soils compared to post-agricultural secondary forest soils may contribute to a higher resilience against environmental changes. Our results advocate for more multifactor global change experiments that investigate the mechanisms underlying the potential effects of land-use legacies on plant-microbe relationships in forest. [ABSTRACT FROM AUTHOR]

Soil organic carbon (SOC) is essential in semi-arid agricultural land for enhancing soil health, particularly through the promotion of microbial activities. This study assessed the impact of different agronomic practices on soil properties, microbial communities, and SOC levels in semi-arid Moroccan wheat fields. Three treatments were investigated: eucalyptus (Eucalyptus spp.) companion planting (EU), and fallowing with harvest residue mulching (FA), with the latter involving both short (3 months; FAS) and long (15 months; FAL) fallow periods. The study revealed significant variation in soil characteristics and microbial communities between these agronomic management regimes. Notably, soils managed with FAL contained elevated SOC levels (1.2%) compared to other treatments (FAS and EU) which show lower SOC range (0.62–0.86%). Both labile C (water-soluble carbon) and recalcitrant C (humic substances) were increased by FAL. Additionally, soil microbial biomass and dehydrogenase activity were observed to be high in FAL-managed soils, along with increased levels of extracellular enzymes related to nutrient cycling (β-glucosidase, alkaline phosphatase, and urease). Phospholipid fatty acid (PLFA) analysis indicated positive correlation between carbon content in soils and microbial populations. In contrast, soils managed with EU had significantly lower SOC levels, possibly due to differences in carbon fractionation. FAL increased soil enzymatic activities and enriched the microbial community when compared to EU management. In conclusion, this study indicated the importance of fallowing and fallowing period for conservation of SOC, and potential to mitigate negative effects of biophysical constraints on agricultural productivity in semi-arid soils of Northwest Africa.

Conventional agricultural practices severely deplete the soil of essential organic matter and nutrients, increasing its vulnerability to disease, drought, and flooding. Permaculture is a form of agroecology adopting a whole ecosystem approach to create a set of principles and design frameworks for enriching soil fertility, but there is little scientific evidence of its efficiency. This study compares two permaculture managed sites with a conventional arable site to investigate the effect of permaculture management on soil fertility. We used phospholipid fatty acid analysis to estimate microbial abundance and diversity and related these to measured soil nutrients and carbon stocks. The potential of permaculture management to mitigate soil greenhouse gas emissions was assessed during a laboratory soil incubation and measurement of greenhouse gases via gas chromatography. Overall, the permaculture managed allotments had three times higher microbial biomass, one and a half times higher nitrogen, and four times higher carbon content than the arable site. Permaculture soils had larger carbon dioxide and nitrous oxide fluxes compared to arable soil, but all sites had a mean negative flux in methane. Permaculture management by use of organic amendments and no-dig practices provides a constant slow release of nutrients and build-up of organic matter and carbon and consequently promotes greater bacterial and fungal biomass within the soil.

Abstract Background Microbial residues are significant contributors to stable soil organic carbon (SOC). Soil aggregates effectively protect microbial residues against decomposition; thus, microbial residue accumulation and distribution among soil aggregates determine long-term SOC stability. However, how tree species influence accumulation and distribution of soil microbial residues remains largely unknown, hindering the chances to develop policies for SOC management. Here, we investigated microbial residue accumulation and distribution in soil aggregates under four subtropical tree species (Cunninghamia lanceolata, Pinus massoniana, Michelia macclurei, and Schima superba) after 29 years of afforestation. Results Accumulation of microbial residues in the 0–10 cm soil layer was 13.8–26.7% higher under S. superba than that under the other tree species. A structural equation model revealed that tree species affected the accumulation of microbial residues directly by altering fungal biomass. Additionally, tree species significantly affected microbial residue distribution and contribution to SOC in the top 20 cm soil. In particular, microbial residue distribution was 17.2–33.4% lower in large macro-aggregates (LMA) but 60.1–140.7% higher in micro-aggregates (MA) under S. superba than that under the other species in the 0–10 cm soil layer, and 14.3–19.0% lower in LMA but 43–52.1% higher in MA under S. superba than that under C. lanceolata and M. macclurei in the 10–20 cm soil layer. Moreover, the contribution of microbial residues to SOC was 44.4–47.5% higher under S. superba than under the other tree species. These findings suggest a higher stability of microbial residues under S. superba than that under the other studied tree species. Conclusions Our results demonstrate that tree species influence long-term microbial persistence in forest soils by affecting accumulation and stabilization of microbial residues.

Holothurians are the dominant megabenthic deposit feeders in the Peru Basin (SE Pacific) and feed to various degrees of selectivity on a heterogenous pool of sedimentary detritus, but drivers of feeding selectivity and diet preferences for most holothurian species are unknown. This study reconstructs the diets of 13 holothurian species of the orders Elasipodida, Holothuriida, and Synallactida. Bulk stable isotope analyses (δ13C, δ15N) of holothurian body wall and gut wall tissues, gut contents, and feces were combined with compound-specific stable isotope analyses of amino acids, phospholipid-derived fatty acids, and neutral-lipid-derived fatty acids in the body wall. We further assessed how holothurians in the Peru Basin partition their resources and calculated how much of the daily particulate organic carbon (POC) flux to the area is ingested by them using information about gut contents of nine species. To assess the dependence of holothurians on fresh phytodetritus, we performed in situ pulse-chase experiments using 13C- and 15N-enriched phytodetritus. By measuring the uptake of this phytodetritus in fatty acids and amino acids and by comparing it with the presence of these compounds in the sediment, we calculated net accumulation and net deficiency for specific fatty acids and amino acids and discussed how climate change might affect the dependence on specific compounds. A Sørensen–Dice coefficient-based cluster analysis using data from trophic levels, levels of heterotrophic re-synthesis of amino acids, feeding selectivity, and food sources/diet suggested two major trophic groups with two optional subgroups each. Species-specific traits of locomotion, tentacle morphology, and gut structure likely allow resource partitioning and differences in selectivity among the holothurians, of which a subpopulation of 65% of all specimens can ingest 4 to 27% of the daily POC flux to the Peru Basin. Holothurians are specifically dependent on the uptake of arachidonic acid from phytodetritus, while most essential amino acids are available in the Peru Basin in sufficient concentrations. [ABSTRACT FROM AUTHOR]

Introduction: Irrigation management dramatically alters soil water availability and distribution and could impact soil microbial communities and carbon (C) and nitrogen (N) cycling to an even greater degree than observed in rainfed systems. Adoption of subsurface drip irrigation (SDI) in California's Mediterranean agroecosystems provides agronomic benefits but wets only a portion of the soil volume near the root zone, leaving the rest dry throughout the growing season. In contrast, traditional furrow irrigation (FI) has periodic wetting events with more homogenous moisture distribution. With conversion to precision irrigation methods, how will the microbiome respond to changes moisture availability, and how is their response influenced by soil C and N resource levels? Methods: In a field experiment in California, we compared SDI and FI's effects on microbial communities and evaluated how long-term organic and conventional management systems impact outcomes. Throughout the growing season, soil samples were collected at two depths (0-15, 15-30 cm) and three distances from bed center (10, 25, 45 cm) where the drip tape is located. Results: At harvest, soils irrigated using SDI had lower microbial biomass C (MBC) than under FI at the surface and showed a build-up of soluble C and N relative to MBC at the bed edge, indicating reduced microbial uptake. Community composition at the bed edge also diverged between SDI and FI, favoring Actinobacteria in the former and Acidobacteria and Gemmatimonadetes in the latter. Regardless of irrigation type, dry areas of the bed had the highest alpha diversity indices. Response to SDI was similar in organic and conventional systems, though organic had higher MBC, DOC, and relative abundance of Proteobacteria and fungal lipids, regardless of irrigation. Discussion: Prolonged dry conditions in SDI appeared to limit microbial access to resources and changed community composition. As seen in non-agricultural systems, the severity and frequency of moisture changes, adaptation of the communities, and resource availability affect microbial response. Decoupling of C and N pools in dry surface soils under SDI may increase the potential for losses of DOC and nitrate with the first winter rains in this Mediterranean climate. [ABSTRACT FROM AUTHOR]

Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats. [ABSTRACT FROM AUTHOR]

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The effects of intensive and reduced tillage, fertilization, and irrigation on soil chemical and microbiological parameters were studied in a long-term field experiment in Hungary. The treatments were plowing tillage, ripper tillage, strip tillage; control (without fertilization), NPK fertilization (N: 160 kg/ha; P: 26 kg/ha; K: 74 kg/ha); and non-irrigation and irrigation. Soil samples were collected through maize monoculture in the fall of 2021 in the 30th year of the experiment. The soil organic carbon, total nitrogen, soil microbial biomass (based on PLFA analysis), and soil enzyme activity were observed to be significantly high in the strip tillage plots, but were lower in the ripper tillage plots, and even lower in the plowing tillage plots. The fungal, arbuscular mycorrhiza fungal, and bacterial biomasses were significantly higher in the strip tillage and ripper tillage plots compared to the plowing tillage plots. The strip tillage treatment was found to be the most favorable cultivation method for improving the microbial biomass and activity of Chernozem soil, followed by the ripper tillage and plowing tillage treatments. The long-term use of chemical fertilizers greatly reduced the soil microbial biomass and negatively impacted the soil microbial community, leading to a decrease in fungi and Gram-negative bacteria. The ratio of cyclopropyl PLFA precursors to cyclopropyl PLFAs, as a “stress factor”, indicated the most stressful bacterial environment was that found in the fertilized, non-irrigated plowed soil.

In recent years, the Sanjiang Plain has experienced drastic human activities, which have dramatically changed its ecological environment. Soil microorganisms can sensitively respond to changes in soil quality as well as ecosystem function. In this study, we investigated the changes in soil microbial community diversity and composition of three typical land use types (forest, wetland and cropland) in the Sanjiang Plain using phospholipid fatty acid analysis (PLFA) technology, and 114 different PLFA compounds were identified. The results showed that the soil physicochemical properties changed significantly (p < 0.05) among the different land use types; the microbial diversity and abundance in cropland soil were lower than those of the other two land use types. Soil pH, soil water content, total organic carbon and available nitrogen were the main soil physico-chemical properties driving the composition of the soil microbial community. Our results indicate that the soil microbial community response to the three different habitats is complex, and provide ideas for the mechanism by which land use changes in the Sanjiang Plain affect the structure of soil microbial communities, as well as a theoretical basis for the future management and sustainable use of the Sanjiang plain, in the northeast of China.

ABSTRACT The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term disposal of high-level nuclear waste. Diversity and temporal changes of bentonite-associated microbial community profiles were assessed under DGR-like conditions for compacted Wyoming MX-80 bentonite (1.25 g/cm3 and 1.50 g/cm3 targeted dry densities) exposed to natural groundwater. Using culture-dependent and molecular techniques, samples taken from the outside layer of 5-year borehole modules revealed up to 66% and 23% of 16S rRNA gene sequences affiliated with Desulfosporosinus and Desulfovibrio, respectively. Putatively involved in sulfate reduction, these taxa were almost undetectable within the bentonite core. Instead, microbial profiles of the inner bentonite core were similar to uncompacted bentonite used to pack modules years earlier, and were consistent with a previously published 1-year time point, revealing no detectable microbial growth. Abundances of culturable aerobic and anaerobic heterotrophic bacteria in the uncompacted bentonite were relatively low, with less than 1,000 and 100 colony-forming units (CFUs) per gram dry weight, respectively. Nearly 5 years after emplacement, culturable heterotrophic bacterial CFUs and sulfate-reducing bacteria did not change significantly inside the bentonite core. Phospholipid fatty acid data indicated similar lipid abundance, and corresponding cell abundance estimates, for inner 5-year MaCoTe bentonite samples compared to those previously obtained for 1-year incubations. Collectively, our results provide complementary evidence for microbial stability inside highly compacted bentonite exposed to conditions that mimic engineered barrier components of a deep geological repository. IMPORTANCE The long-term safety of a deep geological repository for used nuclear fuel is dependent on the performance of the engineered and natural barriers. Microbial activity can produce chemical species that can influence the corrosion of the disposal containers for used nuclear fuel. Although previous studies have evaluated the microbiology of compacted bentonite clay within subsurface environments, these have been limited to relatively short incubations (i.e., 1 year). The current study provides a unique 5-year perspective that reinforces previous findings of growth inhibition for bentonite clay exposed to in situ subsurface conditions.

Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.

The importance of forest floor plants (herbs and mosses) and understory communities on soil C dynamics has been grossly understudied in forest ecosystems; however, there is currently very little knowledge on the impact of forest floor vegetation composition on soil organic C (SOC) accumulation and the microbial metabolic processes. To bridge this gap of knowledge, a forest floor vegetation-removal experiment involving nonvascular mosses (Pleurozium schreberi (PS); Rhizomnium tuomikoskii (RT); and Hylocomiastrum pyrenaicum (HP)) and vascular sedges (Carex sp., CS) was conducted in a subalpine coniferous forest on the eastern edge of Tibetan Plateau, to investigate the associations of different forest floor vegetation communities with mineral soil C accumulation and microbial physiology (C use efficiency (CUE) and microbial biomass turnover). Soils beneath the forest floor vegetative communities differed in soil C and nitrogen (N) concentrations and had distinctively different microbial community structure and physiology. Compared to bare soils, sedge soils had significantly greater SOC and dissolved organic C (DOC) accumulation, greater microbial DNA, biomass C and phospholipid fatty acids (PLFAs) concentrations, and higher microbial CUE and shorter microbial biomass turnover time. While effects of mosses differed among species, P. schreberi had similar effects as sedges, but the effects of H. pyrenaicum and R. tuomikoskii were minimal. Relative to bare soil, P. schreberi and Carex sp. soils were 61.5% and 51.6% higher in microbial CUE and had an obviously shorter microbial biomass turnover time. Variations in the level of DOC and PLFAs (rather than their portion relative to SOC) were the most important regulators of microbial CUE and biomass turnover rate in soils with different forest floor vegetation covers. These results highlight how differences in soil organic matter quality that are directly related to the forest floor vegetation community influence the microbial CUE and biomass turnover and the long-term soil C dynamics.

Litter decomposition is a key ecosystem process that determines rates of carbon and nutrient cycling. Photodegradation and soil-litter mixing have emerged as important drivers of dryland litter decomposition, but how these processes interact with decomposing microorganisms has received less attention. In this study, we examined the effects of ultraviolet-B radiation (UV-B; 280–315 nm) and soil-litter mixing on the decomposition of litter and its associated microbial community in an arid shrubland. We performed a full factorial litter decomposition experiment using leaf litter from a dominant shrub (Prosopis velutina) and a dominant grass (Eragrostis lehmanniana) that were exposed to solar radiation with near-ambient or attenuated UV-B, and were either soil-free or soil-covered; we then quantified litter decomposition and microbial community composition over a 12 month period. In general, shrub litter decomposed more rapidly than grass litter regardless of soil coverage, likely due to its lower C:N. Attenuation of UV-B had modest effects on decomposition but UV-B exposure did increase fungal biomass, perhaps reflecting facilitative aspects of photodegradation. Both bacteria and fungi emerged as important regulators of decomposition, and microbial decomposition was indirectly mediated by litter C:N, soil coverage, and UV-B effects on the microbial community. Bacterial colonization was inhibited in soil-free treatments, but was facilitated when litter was soil-covered. These findings suggest that UV-B may play an important role in facilitating fungal decomposition of litter, while soil-litter mixing is fundamental for promoting bacterial decomposition of litter. Highlights: Soil-litter mixing enhanced bacterial colonization of litter. Fungi are present on dryland litter regardless of soil and UV-B conditions. Soil-litter mixing initially accelerated litter decomposition but subsequently reduced it. [ABSTRACT FROM AUTHOR]

Climate change scenarios predict more frequent and intense drought periods for 2071 to 2100 for many regions of the world including Austria. Current and predicted lower precipitation scenarios were simulated at a lysimeter station containing a fertile and less fertile agricultural soil for 9 years. 13C and 15N-labeled green manure was added in year 8 with the aim to analyze how the predicted precipitation regime affects soil fauna and microbial groups and consequently nitrogen (N) and carbon (C) cycling. Among the investigated mesofauna (collembola and oribatida), the abundance and biodiversity of oribatida was significantly reduced by drought, possibly because they mainly represent K-strategist species with low mobility and consequently the need to adapt to long-term adverse environmental conditions. Microbial community composition and microbial biomass, investigated by phospholipid fatty acid (PLFA) analysis, was indistinguishable between the current and the predicted precipitation scenarios. Nonetheless, soil 13C-CO2 emissions and soil water 15N-NO3 data revealed decelerated mineralization of green manure under reduced precipitation in the first 2 weeks, but no effects were observed on soil C sequestration or on 13C incorporation into microbial PLFAs in the following 1.2 years. We found that over a 1-year time period, decomposition was rather driven by plant residue availability than water limitation of microorganisms in the investigated agroecosystem. In contrast, N2O emissions were significantly reduced under drought, and green manure derived 15N accumulated in the soil under drought, which might necessitate the adjustment of future fertilization regimes. The impacts of reduced precipitation and drought were less pronounced in the more fertile agricultural soil, due to its greater buffering capacity in terms of water storage and organic matter and nutrient availability. [ABSTRACT FROM AUTHOR]

Background: Microbial residues are significant contributors to stable soil organic carbon (SOC). Soil aggregates effectively protect microbial residues against decomposition; thus, microbial residue accumulation and distribution among soil aggregates determine long-term SOC stability. However, how tree species influence accumulation and distribution of soil microbial residues remains largely unknown, hindering the chances to develop policies for SOC management. Here, we investigated microbial residue accumulation and distribution in soil aggregates under four subtropical tree species (Cunninghamia lanceolata, Pinus massoniana, Michelia macclurei, and Schima superba) after 29 years of afforestation. Results: Accumulation of microbial residues in the 0–10 cm soil layer was 13.8–26.7% higher under S. superba than that under the other tree species. A structural equation model revealed that tree species affected the accumulation of microbial residues directly by altering fungal biomass. Additionally, tree species significantly affected microbial residue distribution and contribution to SOC in the top 20 cm soil. In particular, microbial residue distribution was 17.2–33.4% lower in large macro-aggregates (LMA) but 60.1–140.7% higher in micro-aggregates (MA) under S. superba than that under the other species in the 0–10 cm soil layer, and 14.3–19.0% lower in LMA but 43–52.1% higher in MA under S. superba than that under C. lanceolata and M. macclurei in the 10–20 cm soil layer. Moreover, the contribution of microbial residues to SOC was 44.4–47.5% higher under S. superba than under the other tree species. These findings suggest a higher stability of microbial residues under S. superba than that under the other studied tree species. Conclusions: Our results demonstrate that tree species influence long-term microbial persistence in forest soils by affecting accumulation and stabilization of microbial residues. [ABSTRACT FROM AUTHOR]

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Implementing sustainable agricultural land management practices such as no-till (NT) and diversified crops are important for maintaining soil health properties. This study focuses on the soil health of three long-term (44 years) tillage systems, NT, reduced tillage (RT), and conventional tillage (CT), in monoculture winter wheat–fallow (W-F) (Triticum aestivum L.) and wheat–soybean (W-S) (Glycine max (L.) Merrill) rotation. Soil organic carbon (C) was higher in NT than CT in the surface 0–5 cm, but not different in the 5–15 cm, demonstrating SOC stratification on the soil profile. The soil water content was higher in NT followed by RT and CT in the top 0–5 cm. We found an association between increased carbon, aggregation, and AMF biomass. Greater soil aggregation, carbon and AMF were observed in NT at 0–5 cm soil depth. The W-S cropping system had greater soil microbial community composition based on fungi biomass, AMF and fungal to bacteria ratio from phospholipid fatty acid analysis (PLFA). Large macroaggregates were positively correlated with total C and N, microbial biomass, Gram + , and AMF. Soil water content was positively correlated with macroaggregates, total C and N, and AC. No-till increased soil carbon content even after 44 years of cultivation. By implementing conservation tillage systems and diversified crop rotation, soil quality can be improved through greater soil organic C, water content, greater soil structure, and higher AMF biomass than CT practice in the Central Great Plains. [ABSTRACT FROM AUTHOR]

Salt marsh vegetation, mudflat and salt production are common features in worldwide coastal areas; however, their influence on microbial community composition and structure has been poorly studied and rarely compared. In the present study, microbial community composition (phospholipid fatty acid (PLFA) profiling and 16S rRNA gene sequencing (bacterial and archaeal)) and structure, enzymatic activities and abundance of functional genes in the sediments of salt ponds (crystallizer, condenser and reservoir), mudflat and vegetated mudflat were determined. Enzyme activities (β-glucosidase, urease and alkaline phosphatase) were considerably decreased in saltpan sediments because of elevated salinity while sediment of vegetated mudflat sediments showed the highest enzyme activities. Concentrations of total microbial biomarker PLFAs (total bacterial, Gram-positive, Gram-negative, fungal and actinomycetes) were the highest in vegetated mudflat sediments and the lowest in crystallizer sediments. Nonmetric-multidimensional scaling (NMDS) analysis of PLFA data revealed that the microbial community of crystallizer, mudflat and vegetated mudflat was significantly different from each other as well as different from condenser and reservoir. The most predominant phyla within the classified bacterial fractions were Proteobacteria followed by Firmicutes, Bacteroidetes and Planctomycetes, while Euryarchaeota and Crenarchaeota phyla dominated the classified archaeal fraction. Cyanobacterial genotypes were the most dominant in the condenser. Mudflat and vegetated mudflat supported a greater abundance of Bacteroidetes and Actinobacteria, respectively. The results of the present study suggest that salt ponds had significantly decreased the microbial and enzyme activities in comparison to mudflat and vegetated mudflat sediments due to very high salinity, ionic concentrations and devoid of vegetation. The present study expands our understanding of microbial resource utilization and adaptations of microorganisms in a hypersaline environment. [ABSTRACT FROM AUTHOR]

Soil microbial community plays a major role in removal of polycyclic aromatic hydrocarbons (PAHs) from soil, and bioremediation potentially offers an attractive and economic approach to the clean-up of polluted areas. To evaluate the contribution of different microbial groups in soil PAH degradation, enzymatic activity and phospholipid fatty acids (PLFAs) were analysed in a mesocosm trial in three different soils (two natural and one industrial) artificially contaminated with 3- and 5-rings PAHs. The Metabolic Activity Index (MAI) was applied to investigate the microbial community stability, in terms of resistance and resilience. Gram+ and Gram- bacteria were the predominant microbial groups in all soil types. In the first stage of incubation, fungi were predominant in the industrial soil, followed by mycorrhizae and actinomycetes, indicating their stimulation after PAH addition. In the two natural soils, several groups were predominant: actinomycetes in one, fungi and mycorrhizae in the other, indicating a different response of the two natural soils to PAH contamination. Regarding MAI calculated on the enzymatic activities, one natural soil showed a microbial community neither resistant nor resilient in respect to the other and to the industrial soil. Our results highlight that the microbial community changes its composition and then physiological functions according to the land use as a result of PAH addition. [ABSTRACT FROM AUTHOR]

Hydrothermal carbonised wastes (hydrochars) can have toxic effects on soil biota, but factors influencing toxin formation in hydrochar, and subsequent toxicity to soil organisms, have not been elucidated. This study investigated the toxicity of hydrochars on soil biota, with a focus on earthworm (Eisenia fetida) avoidance, microbial metabolic quotient (qCO 2) and microbial activities. Two reaction temperatures (200 °C and 260 °C) and different feedstocks (biosolids, chicken manure and rice straw) were used. Hydrochars produced at 260 °C were highly toxic to earthworms, causing earthworm avoidance of >84 %. Hydrochar from chicken manure and rice straw produced at 200 °C also caused significant avoidance (76–84 %), although with chicken manure, high salt (Na) concentration was the underlying factor rather than toxic organic compounds. In contrast, biosolids hydrochar produced at 200 °C showed no negative effect on earthworms. Further examination of biosolids hydrochar (260 °C) following extraction with water, methanol, acetone-hexane, or sequentially, indicated that toxins causing earthworm avoidance were both polar and non-polar organic compounds, as well as soluble salts. Despite increased qCO 2 suggesting microbial stress, hydrochars generally increased phospholipid fatty acids (bacteria and fungi), soil respiration, enzyme activities and N mineralisation. Findings reveal that while higher temperature hydrochars are highly toxic to earthworms, they do not adversely affect overall soil microbial health. [Display omitted] • Hydrochar was toxic to Eisenia fetida , but microorganisms and microbial functions were unaffected. • High hydrothermal carbonisation temperature (>200 °C) exacerbated hydrochar toxicity. • Toxins in hydrochar can be polar/non-polar organic compounds, or salts (i.e. Na) at high concentration. [ABSTRACT FROM AUTHOR]

A recent innovation in air phytoremediation is active green walls, which utilises biofiltration technology with airflow from mechanical ventilation. While this novel technology is gaining traction, the influence of irrigation on soil moisture, and subsequently the microbial communities that play a role in air filtration is untested. In this study, the application of drip irrigation techniques in active green walls were investigated for their influence on system performance. A modular green wall system was tested, with tests across 7 different plant species, as well as a substrate only control. Water distribution across the modules, the water-carrying capacity and airflow through the substrate were measured. The microbial community present, which is critical to the phytoremediation process, was quantified by identifying individual microbial phospholipid fatty acids (PLFA) within the substrate. Results demonstrated that the lower-speed drip irrigation reduced water consumption compared to the rapid system, and had generally more uniform moisture distribution. High flow drip irrigation resulted in a water pathway phenomenon, leading to uneven moisture distribution within the green wall, and this effect was accentuated with fibrous root plant species. Drip irrigation did not change microbial community composition across planted modules, apart from increasing fungi by 6%, but did wash out bacteria at the high flow rate used (−56.67%), thus low flow rate irrigation rate is more beneficial for both plant growth and microbial community composition. The current work provides evidence that drip irrigation has considerable effects on both substrate airflow rate and substrate microbial density: both key to system air cleaning performance. [Display omitted] • Under drip irrigation, active green walls exhibit uneven soil moisture distribution. • Drip irrigation and plant species impacts airflow in active green walls. • Drip irrigated active green walls can significantly alter temperature and humidity. • Microbial community composition was measured during irrigation. • Irrigation affects substrate Gram-negative bacteria and actinomycetes. [ABSTRACT FROM AUTHOR]

Phosphorus (P) is a limiting nutrient to production in various agricultural ecosystems and many soils contain large amounts of legacy P that is strongly adsorbed on iron (Fe) and aluminum oxides and therefore poorly available to plants. Here we investigate how much mineral-bound P is mobilized in different cropping systems and the influence of agronomic practices on this process. Root ingrowth cores filled with a mix of sand and P-saturated goethite were incubated in the topsoil of: 1) sugar beet in Sweden under sufficient or deficient P additions, 2) perennial Kernza (Thinopyrum intermedium) in Sweden as monoculture or intercropped with Alfalfa with organic management, contrasted to annual winter wheat with inorganic fertilization, and 3) soybean grown in a P-fixing soil in Kenya with or without fertilizer and biochar addition. After one growing season, desorption was evaluated based on the amount of P that remained in the goethite and its ratio with Fe. Possible relationships between the rate of P desorption and abundance of arbuscular mycorrhizal fungi (AMF) were explored by profiling phospholipid fatty acid (PLFA) and neutral lipid fatty acid (NLFA) biomarkers in the sand-goethite mixture collected from the cores. Significant P desorption was found in the rhizosphere of sugar beets under deficient P supply but not in bulk sand-goethite mixture. No P desorption was observed in Kernza as monocrop or intercropped with alfalfa, nor winter wheat. Soybeans had a strong ability to desorb P under all nutrient regimes but significantly more when no fertilizer was applied. In the soybean experiment a significant positive relationship was found between P removal rates and abundance of AMF. These results indicate that strategies for downregulating P application rates and promoting crop-AMF association can be a viable avenue to mobilize legacy P and help make more efficient use of nutrient inputs. At the same time, cropping systems and soil conditions have an overriding influence on the potential P desorption and must therefore be carefully considered during implementation. • Up to 40 % of added P were desorbed from goethite in a cropping system with soybean. • The amount of desorbed P was positively related to the biomass of AMF. • P bound to goethite was also desorbed in the rhizosphere of sugar beet roots. • Reduced nutrient addition enhanced P desorption in soybean and the sugar beet plots. [ABSTRACT FROM AUTHOR]

• Machine learning improves VNIR-MIR models for field-condition soils compared to PLSR. • Cubist, SVM and Ensemble-GLM achieved the most accurate soil property predictions. • EPO improves VNIR-MIR model transfer from pre-treated to field-condition soils. • Models for pre-treated (dried/ground) samples still give the most accurate results. • Machine learning coupled with EPO facilitates on-site VNIR and MIR analysis. Portable visible-to-near-infrared (VNIR) and mid-infrared (MIR) spectroscopy coupled with machine learning can provide detailed and inexpensive information on various key soil properties. However, on-site VNIR and MIR proximal sensing applications are hampered by soil moisture and particle size variations, which distort reflectance spectra collected on field-condition soils and impede the integration of established MIR and VNIR soil spectral libraries in predictive models for field measurements. In this study, we explored the capacity of various machine-learning approaches to calibrate VNIR-MIR models for the prediction of soil organic carbon and phospholipid fatty acid (PLFA)-derived microbial soil properties with field-condition spectral data. We further evaluated the potential to integrate soil spectral libraries into VNIR-MIR proximal sensing applications by testing the transfer of VNIR-MIR models calibrated on pre-treated soil samples to field-condition VNIR-MIR scans using the External Parameter Orthogonalization (EPO) approach to minimize soil moisture and particle size effects. We compiled a diverse soil dataset encompassing a wide range of organic matter content, soil texture, and parent material from soils under grassland and arable land use (n = 175). VNIR-MIR models were used to predict soil organic carbon (SOC), bacterial biomass (BAC), fungal biomass (FUN), and different soil quality indicators (C:N, Fungal-to-bacterial ratio, gram-positive-to-gram-negative ratio) for both field-condition and pre-treated soil spectral data. Calibrations were developed with Partial Least Squares Regression (PLSR), Random Forest (RF), Elastic Net (ENET), Cubist, Support Vector Machines (SVM), and an Ensemble-GLM. We further tested the effectiveness of coupling each machine-learning model with the EPO algorithm to transfer models calibrated on pre-treated soils to field-condition scans. Our results show that machine learning methods such as Cubist and SVM readily outperformed the standard PLSR calibration, with average improvements of ΔRMSE ∼15 % for pre-treated soils and ΔRMSE ∼10 % for field-condition samples. Ensemble-GLM models were about as accurate as the best individual model in each case but did not yield further improvements. The direct calibration transfer from laboratory calibrations to field-condition spectra exhibited very low accuracy. The EPO approach improved model transfer results significantly (ΔRMSE ∼40 %) but was still less accurate than predictive models using spectra from pre-treated soils (ΔRMSE ∼18 %). Our findings highlight the benefits of employing a diverse set of machine-learning algorithms and model ensembles for improved VNIR-MIR calibrations of soil properties and demonstrate that the EPO transform is effective in removing moisture and particle size effects from VNIR and MIR soil spectra collected in field-condition. This opens the opportunity to integrate archived local soil data or extensive soil spectral libraries into proximal soil sensing applications with portable VNIR and MIR spectrometers to facilitate the acquisition of high-quality soil information at high spatiotemporal resolution directly in the field. [ABSTRACT FROM AUTHOR]

The composition of a soil microbial community that is associated with novel rotation crops could contribute to an increased yield of subsequent crops and is an important factor influencing the composition of the rhizosphere microbiome. However, the effect of alternative dryland crops on soil microbial community composition is not clear in the northern Great Plains (NGP). The objective of this study, therefore, was to evaluate the effects of the oilseed crops Ethiopian mustard (Brassica carinata A.) or camelina (Camelina sativa L.) or a 10-species forage/cover crop (CC) mix and fallow on soil biological health. Phospholipid fatty acid (PLFA) analysis was used to characterize the microbial community structure. The results showed that the total bacterial PLFA proportion was significantly higher in camelina and fallow compared to CCs and carinata, whereas the total fungal proportion was significantly higher under a CC mix compared to camelina and fallow. The fungal-to-bacterial ratio was significantly higher in CCs (0.130) and carinata (0.113) compared to fallow (0.088). Fungi are often considered a good indicator of soil health, while bacteria are crucial in soil functions. The changes in specific microbial communities due to crop-related alterations might play a key role in the yield of subsequent crops. This study provides valuable insights into the effect of oilseeds, CCs, and fallow on microbial communities.

Mountain forests are important carbon stocks and biodiversity hotspots but are threatened by increased insect outbreaks and climate‐driven forest conversion. Soil microorganisms play an eminent role in nutrient cycling in forest habitats and form the basis of soil food webs. Uncovering the driving factors shaping microbial communities and functioning at mountainsides across the world is of eminent importance to better understand their dynamics at local and global scales. We investigated microbial communities and their climatic and local soil‐related drivers along an elevational gradient (800–1700 m asl) of primary forests at Changbai Mountain, China. We analyzed substrate‐induced respiration and phospholipid fatty acids (PLFA) in litter and two soil layers at seven sites. Microbial biomass (Cmic) peaked in the litter layer and increased towards higher elevations. In the litter layer, the increase in Cmic and in stress indicator ratios was negatively correlated with Ca concentrations indicating increased nutritional stress in high microbial biomass communities at sites with lower Ca availability. PLFA profiles in the litter layer separated low and high elevations, but this was less pronounced in soil, suggesting that the litter layer functions as a buffer for soil microbial communities. Annual variations in temperature correlated with PLFA profiles in all three layers, while annual variations in precipitation correlated with PLFA profiles in upper soil only. Furthermore, the availability of resources, soil moisture, Ca concentrations, and pH structured the microbial communities. Pronounced changes in Cmic and stress indicator ratios in the litter layer between pine‐dominated (800–1100 m) and spruce‐dominated (1250–1700 m) forests indicated a shift in the structure and functioning of microbial communities between forest types along the elevational gradient. The study highlights strong changes in microbial community structure and functioning along elevational gradients, but also shows that these changes and their driving factors vary between soil layers. Besides annual variations in temperature and precipitation, carbon accumulation and nitrogen acquisition shape changes in microbial communities with elevation at Changbai Mountain. [ABSTRACT FROM AUTHOR]

Plant trait‐based approaches are frequently used to explore the linkages between above‐ground plant communities and below‐ground ecosystem functions. However, the role of plant leaf litter and living root traits in driving soil microbial biomass, community composition and enzyme activities has rarely been explored.Here, we measured the soil microbial biomass, community composition and enzyme activities related to carbon (C), nitrogen (N) and phosphorus (P) acquisition under 3‐year‐old monocultures of 28 common subtropical tree species in China.We found that plant leaf litter and absorptive root traits, including leaf litter C content, litter water holding capacity and root N content, were the three best predictors for soil microbial biomass and enzyme activities. In particular, resource‐exploitative tree species with higher root N contents were associated with microbial communities with lower fungi to bacteria ratios and lower C‐ and P‐acquisition enzyme activities. Tree species with higher leaf litter water holding capacity were associated with microbial resource acquisition strategies for C and P acquisition.Synthesis: Our findings highlighted that plant leaf litter and root traits are important for mechanistically understanding the ecological linkage between the plant community and ecosystem functions. [ABSTRACT FROM AUTHOR]

Black walnut (Juglans nigra) and honeylocust (Gleditsia triacanthos) have gained particular interest for use in silvopastures and other temperate agroforestry systems. However, measures of soil health indicators in these deciduous hardwood silvopastures over time have received limited attention. This study assessed soil health indicators in 25-year-old black walnut- (BSP) and honeylocust-based silvopastures (HSP) and compared with those from adjacent open pasture (OP) systems. Soil samples collected from 0 to 10 cm depth were analyzed for soil organic matter (OM), carbon and nitrogen fractions, glomalin-related soil protein, soil enzymatic activities, and microbial community structure. The soil OM content in HSP (64 g kg−1) was greater (p < 0.05) than BSP and OP (55 g kg−1). The BSP soils had about 45% and 52% more (p < 0.05) microbial biomass carbon and nitrogen than OP soils. The HSP soils had 60% greater (p < 0.05) microbial biomass nitrogen than OP soils. The BSP supported greater (p < 0.05) β-glucosidase and urease activities than the HSP and OP treatments, while greater (p < 0.05) β-glucosidase activity was measured in HSP than OP. Total phospholipid-derived fatty acid and actinomycetes abundance were greater (p < 0.001) in OP compared to BSP and HSP while the arbuscular mycorrhiza fungi abundance was greater (p < 0.05) in OP than in HSP. These findings indicate that black walnut and honeylocust trees in the silvopastures with proper management can improve certain soil health parameters over time depending on tree characteristics and the age of the system. [ABSTRACT FROM AUTHOR]

To analyze the rhizosphere bacterial communities in wetlands, the total lipid content was extracted from a peat soil and 4 abundant wetland plant roots (Typha angustifolia L., Salix cinerea L., Carex pseudocyperus L., Thelypteris palustris Salisb.). The separated phospholipid fraction was further fractionated and derivatized prior to gas chromatography-mass spectrometry (GC-MS) measurement. In the evaluation only the bacteria-specific fatty acids were used in order to neglect fatty acid information derived from plant root cells. Based on these analyses, a high level bacterial concentration was demonstrated in the rhizosphere, and the relative occurrence of aerobe and anaerobe, Gram positive and negative bacteria, methanotrophs, sulphate reducers and Actinobacteria was determined. Through the PLFA analysis the study of bacteria regardless of culturability was possible. [ABSTRACT FROM AUTHOR]

The wetlands in China's Sanjiang Plain have experienced intensive anthropogenic disturbance recently, and this has obviously changed their environmental characteristics. Soil microorganisms play an important role in wetland ecosystems. However, the effects of different wetland types on soil microbial diversity and community composition remain largely unclear. Therefore, we assessed the effects of three typical wetland types—permanently flooded wetlands, seasonally flooded wetlands and non-flooded wetlands—on soil microbial communities in the Sanjiang Plain, using phospholipid fatty acid analysis (PLFA) technology. A total of 56 different PLFA compounds were identified, of which 10 are typically produced by uncharacterized bacteria, 15 by Gram-positive bacteria, and 11 by Gram-negative bacteria. In addition, 2 fungal groups were identified, based on four PLFAs, and four PLFAs typical for protozoa were detected. High levels were detected for 16:0 (attributed to bacteria) and i17:1ω9c (produced by Gram-positive bacteria). The latter (i17:1ω9c) was exceptionally high in non-flooded soil (8407.15 ± 2675.84 ng/g). High levels of 18:1ω7c (1939.15 ± 666.13 ng/g) and 18:1ω9c (1713.26 ± 360.65 ng/g) were detected in permanently flooded wetlands and about the same in seasonally flooded wetlands, but lower ranks were present in the drier non-flooded wetlands. The Shannon-Wiener diversity index decreased with permanently flooded wetlands (3.05) > seasonally flooded wetlands (3.02) > non-flooded wetlands (2.12). Redundancy analysis showed that the two axes could explain a total of 94.48% of soil microbial communities. Soil water content, total and available phosphorus, and total and available nitrogen correlated significantly with soil microbial communities of three wetland types. Cluster analysis of correlations between individual PLFA biomarkers and soil physiochemical properties demonstrated the complexity of the community responses to the three different habitats. This study demonstrates that microbial diversity and composition changed sensitivity among the three wetland types, and soil moisture content was the key environmental factor to affect the soil microbial communities. [ABSTRACT FROM AUTHOR]

Manure is a key source of N for crops, especially in organic farming systems, but also a driver of N2O emissions from soil. Treatment technologies removing manure organic matter affect soil N2O emissions, but the direction and magnitude of these effects remain uncertain. We explored the effects of four fertilizer materials derived from cattle manure on soil N2O emissions. Treatments included: untreated cattle manure (CA), cattle manure co-digested with grass-clover silage (DD); a liquid fraction (LF) produced by mechanical separation of digestate; and a concentrated fertilizer with NH4+-N and sulfate (NS) produced from stripped H2S and NH3. These fertilizers were surface-applied to a sandy loam (Foulum) and a clay loam soil (Askov) at 55% water-filled pore space (WFPS) in 28-day laboratory experiments with monitoring of CO2 and N2O. Samples were sectioned during or after incubation to describe mineral N and microbial dynamics. Although the WFPS in both soils was 58–61%, N2O emissions varied greatly, and this was explained by differences in water potential, and in the relative gas diffusivity which was approx. 0.011 and 0.030 in Foulum and Askov soil, respectively. Unexpectedly, treatment LF with the lowest manure organic matter input had the highest N2O emissions. Denitrification was the main pathway producing N2O as determined by 15N enrichment of soil NO3−. The vertical distribution of mineral N and microbial activities, and PLFA, indicated that N2O emissions from the organic fertilizers depended on their interaction with the soil, as modified by soil water potential and gas diffusivity at the time of application. [ABSTRACT FROM AUTHOR]

This study was conducted in order to understand the effects of land use and soil types on microbial activity and community structure. Soil samples were collected from four different soil types (Solonetz, Solonchak, Chernozem and Gleysol) being used under different land use practices (arable, pasture and meadow). The soil chemical properties, moisture content, microbiological activity and community size were investigated. The principal component analysis results showed that different land uses and soil types are clearly separated based on the chemical properties of the soil. The canonical correspondence analysis results revealed that more than 78% of variation in the microbiological properties of the samples could be explained by environmental factors. Significant biological differences were observed among the different land use practices and soil types, and also soil cultivation affected the different groups of soil microbes. Sampling sites were separated into two main clusters (BrayCurtis) based on certain microbiological properties, salt-affected and non-salt-affected soils. The soil types were the main driving factor, with high soil taxonomic distances, however, low taxonomic distances indicated that land use had more pronounced effects on soil microbiological properties. [ABSTRACT FROM AUTHOR]

Soil microorganisms and dissolved organic matter (DOM) play vital roles in nutrient cycling and maintaining plant diversity. The aim of this study was to clarify the relationship between DOM component characteristics and microbial community structure in the soil of Larix principis-rupprechtii Mayr. plantations. We quantified the responses of the soil microbial and DOM characteristics to stand age in a plantation forest ecosystem using phospholipid fatty acid (PLFA) analyses, ultraviolet-visible spectroscopy, and fluorescence spectroscopy. Three humic-like components and a fulvic-like component were identified from the soil samples, and humic-like substances were the dominant component of the soil DOM of the stands of different ages. The fluorescence index showed that the sources of soil DOM in the stands of different ages throughout the growth stages may be mostly plant residues, with very little contribution from microbial sources. Furthermore, the results demonstrated that stand age and growth season had a significant effect on the contents of the soil PLFA biomarkers of L. principis-rupprechtii Mayr. Additionally, significantly higher contents of different species of soil PLFA biomarkers were observed in the young forest (17a) than in the sapling forest (7a) and half-mature forest (27a), suggesting that stand age differences in the quality and quantity of larch litter and soil physicochemical characteristics affect the microbial community structure. Redundancy analysis (RDA) showed that changes in the soil DOM quality and components that were driven by growth season and stand age were the major drivers of variations in the soil microbial community structure in the study region. Overall, the seasonal variations in DOM quality and components may contribute to the variability of soil microorganisms, and the soil microbial responses to tree age will depend upon the provisioning of these resources. [ABSTRACT FROM AUTHOR]

Dumped waste is not only a problem from an aesthetic point of view, but also has an environmental polluting effect, or can even pose a direct danger if the waste is dumped in illegal landfills in an uncontrolled manner with unknown composition. In the case of soil pollution, the assessment of the changing microbial state can be used as an indicator of initial changes, since waste as a pollutant impacts the diversity of the landfill's microbial community. The degree of change depends on the qualitative and quantitative composition of the pollutants, which can be measured through the microbial phospholipid fatty acid (PLFA) pattern. The aim was a comprehensive assessment of the soil microbiological and toxicological hazards of various illegal landfill. Cluster-analysis of the average principal component revealed significant differences between the experimental sites. In comparison with the control site, the percentage of fatty acid biomarkers of Gram-positive bacteria was significantly higher in the contaminated areas, as well as the ratio of trans/cis isomerization in the case of 16:1ω7 and 18:1ω7 fatty acids. The inverse tendency was observed in the relative quantities of fatty acid biomarkers of Gram-negative bacteria compared to Actinomycetes, and in the fungal-bacterial ratio. [ABSTRACT FROM AUTHOR]

Soil translocation is an ecological habitat restoration technique, which consists of moving the entire topsoil from a donor site to a chosen receptor site. We investigated soil chemistry and microbiology changes three growing seasons after the salvage of semi‐ancient woodland soil (0.94 ha) to a nearby receptor pasture due to road widening works (Kent, United Kingdom). We sampled (1) Intact woodland soils adjacent to the area of soils that was translocated to represent the lost donor site; (2) The soil from three growing seasons after it had been translocated; and (3) Grassland soils adjacent to the translocated soil to represent the original receptor site. The intention was to ascertain if shifts in soil chemistry and microbial community composition (phospholipid fatty acid analysis, PLFA) occurred due to soil translocation. PLFA signature biomarkers demonstrated the overall microbial community profile of the translocated and woodland soils were similar; however, salvaged soils had a 40% increase in the arbuscular mycorrhizal fungi bioindicator fatty acid 16:1ω5, a 10% decrease in the Gram‐positive bacterial fatty acids, and increased pH (5.01–5.77) compared to the original donor woodland soil. Microbial community composition (PLFA) correlated well with soil pH across all sites. Considering that pH increases with soil depth in this location, it is likely that mixing of soil horizons during translocation increased the topsoil pH causing changes in the soil microbial communities. We concluded that after three growing seasons, the chemical and microbial properties of the salvaged soil were characteristic of a woodland soil but showed signs of disturbance. [ABSTRACT FROM AUTHOR]

The impact of land consolidation on the soil microbial PLFA diversity is of great importance for understanding the effective arable land usage, improving agricultural ecological conditions and environment. In this study, we collected the soil samples (0-20 cm) in experimental plots with 0 (Z0), 1 (Z1a) and 4 (Z4a) years of land consolidation in the forest station of Ningbo City, Zhejiang Province, southeastern China. The results were analyzed using ANOVA for randomized block design. Compared with control (Z0), the soil pH value under Z1a treatment increased by 14.6%, soil organic carbon (SOC) content decreased by 65.4%, so did the PLFA contents and relative abundance of all the microbial PLFA diversity (P < 0.05), respectively. Meanwhile, for the Z1a treatment, the ratio of fungi to bacteria (F/B) significantly decreased by 35.9% (P < 0.05), while the ratio of Gram-positive bacteria to Gram-negative bacteria (G+/G-) signific antly increased by 56.1%. This was strongly related to the increased soil pH values and the decrease of SOC. The Shannon index (H) and evenness index (E) of soil microbial PLFA diversity were significantly decreased after land consolidation (P < 0.05). Compared to the Z1 treatment, the microbial PLFA diversity was improved slightly. Therefore, the land consolidation could significantly affect the composition of soil microbial PLFA diversity, and decrease the soil ecosystem stability. [ABSTRACT FROM AUTHOR]

Perennial cropping plays a vital role in regulating soil carbon sequestration and thus mitigating climate change. However, how perennial cropping affects the soil microbial community remains elusive. Using a field investigation, this study was conducted to examine the effects of mugwort cropping along a chronosequence (that is, wheat–maize rotation, 3-year, 6-year, and 20-year mugwort cropping) on a soil microbial community in temperate regions of Northern China. The results showed that the highest total, actinomycete, and fungi phospholipid fatty acids (PLFAs) were found in the 3-year mugwort cropping soils. By contrast, all PLFAs of microbial groups were lowest in the 20-year mugwort cropping soils. Network complexity of the soil microbial community under each of the three durations of mugwort cropping was greater than that under the wheat–maize rotation. Changes in total nitrogen and phosphorus content as well as the ratio of ammonium nitrogen to nitrate nitrogen primarily explained the variations in soil microbial community along the mugwort cropping chronosequence. Our observations highlight the contrasting responses of soil microbial community to short-term and long-term mugwort cropping compared with conventional rotations and would have critical implications for sustainable agricultural management under perennial cropping in temperate regions. [ABSTRACT FROM AUTHOR]