Search

It is well established that land use change (LUC) can impact soil organic carbon (SOC) in tropical regions, but the long-term effects of LUC on soil quality and C cycling remain unclear. Here, we evaluated how LUC affects soil C cycling in the Amazon region using a 100-year observational chronosequence spanning primary forest-to-pasture conversion and subsequent secondary forest succession. We found a surprising increase in topsoil SOC concentrations 60 years following conversion, despite major losses (> 85%) of forest-derived SOC within the first 25 years. Shifts in molecular composition of SOC, identified with diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, occurred in tandem with a significant decline in permanganate-oxidizable C (POXC) and β-glucosidase activity (per unit SOC), interpreted as a deceleration of soil C cycling after pasture grasses became the dominant source of C inputs to soil. Secondary forest succession caused rapid reversal to conditions observed under primary forest for β-glucosidase activity but not for SOC molecular composition (DRIFT spectroscopy), reflecting a long-lasting effect of LUC on soil C cycling. Our results show that rapid changes in the origin of SOC occur following deforestation with legacy effects on some indicators of C cycling (e.g. enzyme activity) but not others (e.g. molecular composition). This approach offers mechanistic understanding of LUC in the Amazon basin and can be used to help explain conflicting reports on how deforestation impacts SOC in the region.

Most restoration projects involving invasive plant eradication tend to focus on plant removal with little consideration given to how these invasives change soil microbial communities. However, soil microorganisms can determine invasibility of habitats and, in turn, be altered by invasives once established, potentially inhibiting native plant establishment. We studied soil microbial communities in coastal dunes with varying invasion intensity and different restoration approaches (herbicide, mechanical excavation) at Point Reyes National Seashore. Overall, we found evidence of a strong link between bacterial and fungal soil communities and the presence of invasives and restoration approach. Heavily invaded sites were characterized by a lower abundance of putatively identified nitrifiers, fermentative bacteria, fungal parasites, and fungal dung saprotrophs and a higher abundance of cellulolytic bacteria and a class of arbuscular mycorrhizal fungi (Archaeosporomycetes). Changes in soil microbiota did not fully dissipate following removal of invasives using herbicide, with exception of reductions in cellulolytic bacteria and Archaeosporomycetes abundance. Mechanical restoration effectively removed both invasives and soil legacy effects by inverting or “flipping” rhizome-contaminated surface soils with soils from below and may have inadvertently induced other adverse effects on soils that impeded reestablishment of native dune plants. Land managers should consider additional measures to counteract lingering legacy effects and/or focus restoration efforts in areas where legacy effects are less pronounced.

Biochar greatly influences the soil bacterial community and nutrient transformations, while our knowledge of the responses of fungal lifestyles to biochar is still in its infancy. Here, we used experimental pre-treatments (acetone extraction) of nutrient-rich biochars to identify which major biochar properties influence fungi the most: the easily mineralizable C, fused aromatic backbone, or the inorganic nutrients of biochars. Our objective was to investigate how different biochar fractions (easily mineralizable C, fused aromatic C, nutrients) structure the fungal taxonomic and functional communities. The easily mineralizable C of biochars induced greater short-term changes in fungal community composition compared to the fused aromatic C. The easily mineralizable C significantly decreased the relative abundance of Basidiomycota by avg. 10.6%, while it had no effects on Ascomycota and Zygomycota. Co-occurrence network indicated that saprophytic fungi were self-assembled in the easily mineralizable C-sufficient environment, whereas they were the connectors to interact with other groups when lower amounts of energy in form of mineralizable C were present. Thus, the easily mineralizable C in biochar as a microbial C source probably promoted saprotroph growth, caused them to self-assemble and to enhance their competitive capacity, leading to overall diversity decrease and relative decline of fungal pathogens. The inorganic nutrients had no effects on fungal diversity and saprotroph abundance, while they decreased the relative abundance of Zygomycota. Our study highlighted the important roles of both mineralizable C and inorganic nutrients in modification of the fungal community, and demonstrated that biochar probably favors the growth of saprotrophs over soil-borne fungal pathogens.

AimsTo identify and characterize the lysis gene cassette from the bacteriophage ST79 that lyses Burkholderia pseudomallei.Methods and resultsApproximately 1·5 kb of ST79 lysis genes were identified from the phage genome data. It was composed of holin, peptidase M15A or endolysin, lysB and lysC. Each gene and its combinations were cloned into Escherichia coli and the lytic effects were measured. Co-expression of holin and peptidase M15A showed the highest lysis activity. Expression of holin, lysB/C or holin-peptidase M15A-lysB/lysC lysed the E. coli membrane, whereas peptidase M15A alone did not. The predicted transmembrane structures of holin and lysB/C indicated that they could be inserted into the bacterial membrane to form pores, affecting cell permeability and causing lysis.ConclusionThis is the first report of an investigation into the lysis genes of B. pseudomallei's lytic phage using E. coli as a model.Significance and impact of the studyBurkholderia pseudomallei, a Gram-negative bacterium causing an infectious disease, is intrinsically resistant to several antibiotics, and a vaccine is not available. The lysis genes of ST79, the first reported lytic bacteriophage of B. pseudomallei, were characterized. The development of ST79 as an alternative treatment for skin ulceration, for example, or to be used as a gene cloning tool for B. pseudomallei may be possible with this knowledge.

Seasonal floodplains in the Amazon basin are important sources of methane (CH 4 ), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH 4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH 4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH 4 fluxes. CH 4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH 4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH 4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH 4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH 4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH 4 oxidation pathways in mitigating CH 4 emissions in Amazonian floodplains., (© 2024. The Author(s).)

Deforestation of tropical rainforests is a major land use change that alters terrestrial biogeochemical cycling at local to global scales. Deforestation and subsequent reforestation are likely to impact soil phosphorus (P) cycling, which in P-limited ecosystems such as the Amazon basin has implications for long-term productivity. We used a 100-year replicated observational chronosequence of primary forest conversion to pasture, as well as a 13-year-old secondary forest, to test land use change and duration effects on soil P dynamics in the Amazon basin. By combining sequential extraction and P K-edge X-ray absorption near edge structure (XANES) spectroscopy with soil phosphatase activity assays, we assessed pools and process rates of P cycling in surface soils (0-10 cm depth). Deforestation caused increases in total P (135-398 mg kg -1 ), total organic P (P o ) (19-168 mg kg -1 ), and total inorganic P (P i ) (30-113 mg kg -1 ) fractions in surface soils with pasture age, with concomitant increases in P i fractions corroborated by sequential fractionation and XANES spectroscopy. Soil non-labile P o (10-148 mg kg -1 ) increased disproportionately compared to labile P o (from 4-5 to 7-13 mg kg -1 ). Soil phosphomonoesterase and phosphodiesterase binding affinity (K m ) decreased while the specificity constant (K a ) increased by 83%-159% in 39-100y pastures. Soil P pools and process rates reverted to magnitudes similar to primary forests within 13 years of pasture abandonment. However, the relatively short but representative pre-abandonment pasture duration of our secondary forest may not have entailed significant deforestation effects on soil P cycling, highlighting the need to consider both pasture duration and reforestation age in evaluations of Amazon land use legacies. Although the space-for-time substitution design can entail variation in the initial soil P pools due to atmospheric P deposition, soil properties, and/or primary forest growth, the trend of P pools and process rates with pasture age still provides valuable insights., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier GmbH. All rights reserved.)

Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH 4 ) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH 4 cycle. To better predict the responses of soil CH 4 -cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH 4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH 4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH 4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH 4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH 4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Understanding the effects of forest-to-agriculture conversion on microbial diversity has been a major goal in soil ecological studies. However, linking community assembly to the ruling ecological processes at local and regional scales remains challenging. Here, we evaluated bacterial community assembly patterns and the ecological processes governing niche specialization in a gradient of geography, seasonality, and land-use change, totaling 324 soil samples, 43 habitat characteristics (abiotic factors), and 16 metabolic and co-occurrence patterns (biotic factors), in the Brazilian Atlantic Rainforest, a subtropical biome recognized as one the world's largest and most threatened hotspots of biodiversity. Pairwise beta diversities were lower in pastures than in forest and no-till soils. Pasture communities showed a predominantly neutral model, regarding stochastic processes, with moderate dispersion, leading to biotic homogenization. Most no-till and forest microbial communities followed a niche-based model, with low rates of dispersal and weak homogenizing selection, indicating niche specialization or variable selection. Historical and evolutionary contingencies, as represented by soil type, season, and dispersal limitation were the main drivers of microbial assembly and processes at the local scale, markedly correlated with the occurrence of endemic microbes. Our results indicate that the patterns of assembly and their governing processes are dependent on the niche occupancy of the taxa evaluated (generalists or specialists). They are also more correlated with historical and evolutionary contingencies and the interactions among taxa (i.e., co-occurrence patterns) than the land-use change itself., (© 2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.

The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize ( Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH 4 ), carbon dioxide (CO 2 ), and nitrous oxide (N 2 O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes ( mcrA , pmoA , nifH , and nosZ ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N 2 O emissions around 1 week after application; I tended to reduce CH 4 and CO 2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO 2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Yoshiura, Venturini, Braga, França, Lyra, Tsai and Rodrigues.)

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH 4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH 4 emissions across floodplain areas. Here, we report the in situ composition of CH 4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH 4 cycling groups. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. Methanotrophs known to use different pathways to oxidise CH 4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry but also the composition of the microbial communities. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH 4 emissions in the region., (© 2021 John Wiley & Sons Ltd.)

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales , Chitinophagaceae , and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH 4 ) emission. To better understand the drivers of this change, we measured soil CH 4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH 4 (mean: 3454.6 ± 9482.3 μg CH 4 m -2 d -1 ), consistent with previous reports, while forest soils on average emit CH 4 at modest rates (mean: 9.8 ± 120.5 μg CH 4 m -2 d -1 ), but often act as CH 4 sinks. We report that secondary forest soils tend to consume CH 4 (mean: -10.2 ± 35.7 μg CH 4 m -2 d -1 ), demonstrating that pasture CH 4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH 4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH 4 . Each land use type had a unique subset of taxa associated with CH 4 flux, suggesting that land use change alters CH 4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH 4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO 2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment. IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests., (Copyright © 2020 American Society for Microbiology.)

Lignocellulose comprises a significant portion of municipal solid waste (MSW) - 40-70% in developed countries, including paper, wood, and yard waste. Cellulose and hemicellulose are often shielded by lignin, posing a barrier to waste decomposition and landfill gas generation. Unfortunately, lignin is resistant to microbial degradation under low-oxygen conditions that normally occur in MSW landfills. The bacterium strain TAV5, microaerophilic and member of phylum Verrucomicrobia, isolated from the hindgut of the Reticulitermes flavipes termite, the most widely distributed subterranean termite in North America. Its genome contains genes associated with methylotrophic competency which code for enzymes that structurally modify lignin. The overall goal of this research was to use TAV5 to modify lignin and boost methane production from MSW. Batch-scale reactors (125 mL) were filled with paper, yard, or wood waste, and four ratios of mixed of waste. Reactors were seeded with different ratios of TAV5 to anaerobic digester (AD) microorganisms (representing landfill anaerobic microorganisms). Based on batch tests, optimal ratios of TAV5 to AD microorganisms were used to seed wastes (mixed, yard, and wood) in 6-gallon reactors. Addition of TAV5 increased methane production from mixed waste, yard waste, and wood, by 49%, 34%, and 297%, respectively. TAV5 decreased acid soluble lignin by 7-39%, depending on waste type. TAV5 grown under aerobic conditions and room temperature (not requiring a heated anaerobic chamber) was found to remain viable and increase methane production under low-level oxygen conditions (1-2%). This finding will potentially lessen costs for growing large volumes of it for seeding landfills., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains., (Copyright © 2020 Kotak et al.)

Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

Syntheses of large datasets have allowed increased clarity of distribution patterns and variation in soil major and trace elements. However, the drivers of variation in topsoil elements across biogeographical scales are not well understood. Our aim was to (1) identify how landscape-scale climate, geographical features, and edaphic factors influence soil elements, and (2) determine key environmental thresholds for shifts in soil element concentration. We analyzed patterns of variation in topsoil elements using 9830 samples collected across 39,000km 2 in subtropical land in southeast China. Canonical correlations and multiple linear regressions were used to model variations of each element across mean annual temperature (MAT), mean annual precipitation (MAP), land use, spatial topography, and soil pH. Element concentrations show significant latitudinal and longitudinal trends, and are significantly influenced by climate, land use, spatial topography, and soil pH. Longitude, pH, MAT, and MAP were the environmental factors most tightly correlated with element concentrations. Climate and soil pH drove positive or negative alterations in soil elements, with threshold indicators of MAP=1000mm/1500mm, MAT=17.8°C/18.0°C, and pH=5.8/5.0, respectively. Our results indicate topsoil elements have structural and functional thresholds of climate and soil pH in relatively wet and acidic environments. Our findings can facilitate holistic soil element concentration predictions and help elucidate the specific influences of climate and soil pH, enabling development of more complete biogeochemical models., (Copyright © 2018. Published by Elsevier B.V.)

The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time., (© FEMS 2019.)

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (-0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

We report here the near-complete genome sequence of " Candidatus Spirobacillus cienkowskii," a spiral-shaped, red-pigmented uncultivated bacterial pathogen of Daphnia spp. The genome is 2.74 Mbp in size, has a GC content of 32.1%, and contains genes associated with bacterial motility and the production of carotenoids, which could explain the distinctive red color of hosts infected with this pathogen.

Burkholderia pseudomallei is a Gram-negative bacterium found in soil and the causative agent of a severe disease in humans and animals known as melioidosis. It is intrinsically resistant to many antibiotics and has been reported resistant to the drugs of choice; ceftazidime. Microbial communities in soil in the presence and absence of B. pseudomallei were investigated using metagenomics approach. The variation in bacterial species diversity was significantly higher in soil samples without B. pseudomallei. Abundances of phyla Actinobacteria and Firmicutes were found significantly higher in B. pseudomallei-negative soils. Bacillus amyloliquefaciens KKU1 in phylum Firmicutes was discovered from negative soil and its secondary metabolites could inhibit clinical, environmental and drug resistant isolates of B. pseudomallei, together with some pathogenic Gram-negative but not Gram-positive bacteria. The antimicrobial activity from KKU 1 against B. pseudomallei was abolished when treated with proteinase K, stable in a wide range of pH and remained active after heating at 100 °C for 15 min. Precipitated proteins from KKU1 were demonstrated to cause lysis and corrugated surfaces of B. pseudomallei. The minimum inhibitory concentrations and minimum bactericidal concentrations of the precipitated proteins from KKU1 against B. pseudomallei were 0.97 μg/ml and 3.9 μg/ml. Interestingly, Native SDS-PAGE showed small active compounds of less than 6 kDa, along with other information collectively suggesting the properties of antimicrobial peptides. For the first time, culture-independent information in melioidosis endemic area could lead to a suspected source of metabolites that may help defense against B. pseudomallei and other pathogenic Gram-negative bacteria.

Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.

Cyanobacteria-dominated harmful algal blooms are increasing in occurrence. Many of the taxa contributing to these blooms are capable of fixing atmospheric nitrogen and should be favored under conditions of low nitrogen availability. Yet, synthesizing nitrogenase, the enzyme responsible for nitrogen fixation, is energetically expensive and requires substantial concentrations of iron. Phosphorus addition to nitrogen poor streams should promote nitrogen fixation, but experimental results so far have been inconclusive, suggesting that other factors may be involved in controlling this process. With iron potentially limited in many streams, we examined the influence of phosphorus-iron colimitation on the community structure of nitrogen-fixing organisms. In stream microcosms, using microscopic and molecular sequence data, we observed: (i) the greatest abundance of heterocyst forming nitrogen-fixing cyanobacteria in low nitrogen treatments with high phosphorus and iron and (ii) greater abundance of non-photosynthetic nitrogen-fixing bacteria in treatments with nitrogen compared to those without it. We also found that comparisons between molecular results and those obtained from microscopic identification provided complementary information about cyanobacterial communities. Our investigation indicates the potential for phosphorus-iron colimitation of stream nitrogen-fixing organisms.

Grazing and topography have drastic effects on plant communities and soil properties. These effects are thought to influence arbuscular mycorrhizal (AM) fungi. However, the simultaneous impacts of grazing pressure (sheep ha -1 ) and topography on plant and soil factors and their relationship to the production of extra-radical AM hyphae are not well understood. Our 10-year study assessed relationships between grazing, plant species richness, aboveground plant productivity, soil nutrients, edaphic properties, and AM hyphal length density (HLD) in different topographic areas (flat or sloped). We found HLD linearly declined with increasing grazing pressure (1.5-9.0 sheep ha -1 ) in sloped areas, but HLD was greatest at moderate grazing pressure (4.5 sheep ha -1 ) in flat areas. Structural equation modeling indicates grazing reduces HLD by altering soil nutrient dynamics in sloped areas, but non-linearly influences HLD through plant community and edaphic changes in flat areas. Our findings highlight how topography influences key plant and soil factors, thus regulating the effects of grazing pressure on extra-radical hyphal production of AM fungi in grasslands. Understanding how grazing and topography influence AM fungi in semi-arid grasslands is vital, as globally, severe human population pressure and increasing demand for food aggravate the grazing intensity in grasslands.

We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential., (© FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The use of culture-independent approaches, such as metagenomics, provides complementary access to environmental microbial diversity. Mangrove environments represent a highly complex system with plenty of opportunities for finding singular functions. In this study we performed a functional screening of fosmid libraries obtained from an oil contaminated mangrove site, with the purpose of identifying clones expressing hydrolytic activities. A novel gene coding for a β- N -acetylhexosaminidase with 355 amino acids and 43KDa was retrieved and characterized. The translated sequence showed only 38% similarity to a β- N -acetylhexosaminidase gene in the genome of Veillonella sp. CAG:933, suggesting that it might constitute a novel enzyme. The enzyme was expressed, purified, and characterized for its enzymatic activity on carboxymethyl cellulose, p-Nitrophenyl-2acetamide-2deoxy-β-d-glucopyranoside, p-Nitrophenyl-2acetamide-2deoxy-β-d-galactopyranoside, and 4-Nitrophenyl β-d-glucopyranoside, presenting β- N -acetylglucosaminidase, β-glucosidase, and β-1,4-endoglucanase activities. The enzyme showed optimum activity at 30 °C and pH 5.5. The characterization of the putative novel β- N -acetylglucosaminidase enzyme reflects similarities to characteristics of the environment explored, which differs from milder conditions environments. This work exemplifies the application of cultivation-independent molecular techniques to the mangrove microbiome for obtaining a novel biotechnological product., Competing Interests: The authors declare no conflict of interest. The founding sponsors had role in the collection of samples and support in the publication of the results.

The lytic phage ST79 of Burkholderia pseudomallei can lyse a broad range of its host including antibiotic resistant isolates from within using a set of proteins, holin, lysB, lysC and endolysin, a peptidoglycan (PG) hydrolase enzyme. The phage ST79 endolysin gene identified as peptidase M15A was cloned, expressed and purified to evaluate its potential to lyse pathogenic bacteria. The molecular size of the purified enzyme is approximately 18 kDa and the in silico study cited here indicated the presence of a zinc-binding domain predicted to be a member of the subfamily A of a metallopeptidase. Its activity, however, was reduced by the presence of Zn(2+). When Escherichia coli PG was used as a substrate and subjected to digestion for 5 min with 3 μg/ml of enzyme, the peptidase M15A showed 2 times higher in lysis efficiency when compared to the commercial lysozyme. The enzyme works in a broad alkaligenic pH range of 7.5-9.0 and temperatures from 25 to 42 °C. The enzyme was able to lyse 18 Gram-negative bacteria in which the outer membrane was permeabilized by chloroform treatment. Interestingly, it also lysed Enterococcus sp., but not other Gram-positive bacteria. In general, endolysin cannot lyse Gram-negative bacteria from outside, however, the cationic amphipathic C-terminal in some endolysins showed permeability to Gram-negative outer membranes. Genetically engineered ST79 peptidase M15A that showed a broad spectrum against Gram-negative bacterial PG or, in combination with an antibiotic the same way as combined drug methodology, could facilitate an effective treatment of severe or antibiotic resistant cases.

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98% minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65.2%) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10.9%), Spirochaetes (4.3%), Bacteroidetes (6.5%), Actinobacteria (2.2%) and Deferribacteres (2.2%). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.