Bacterial community composition of divergent soil habitats in a polar desert

Sediment Bacteria in the Alpine Lake Sayram: Vertical Patterns in Community Composition

Bacterial communities inhabiting alpine lakes are essential to our understanding of ecosystem processes in a changing climate, but little has been reported about the vertical patterns of sediment bacterial communities in alpine lakes. To address this knowledge gap, we collected the 100 cm long sediment core from the center of Lake Sayram, the largest alpine lake in Xinjiang Uygur autonomous area, China, and used 16S rRNA gene-targeted amplicon sequencing to examine the bacterial populations. The results showed that bacterial diversity, as estimated by the Shannon index, was highest at the surface (6.9849 at 0-4 cm) and gradually decreased with depth up to 3.9983 at 68-72 cm, and then increased to 5.0927 at 96-100 cm. A total of 56 different phyla and 1204 distinct genera were observed in the sediment core of Lake Sayram. The bacterial community structure in the sediment samples from the various layers was dissimilar. The most abundant phyla in alpine Lake Sayram were Proteobacteria, Firmicutes, and Planctomycetes, accounting for 73%, 6%, and 4% of the total reads, respectively; the most abundant genera were Acinetobacter, Hydrogenophaga, and Pseudomonas, accounting for 18%, 12%, and 8% of the total reads, respectively. Furthermore, the relative abundance of Acinetobacter increased with sediment depth, while the relative abundance of Hydrogenophaga and Pseudomonas decreased with sediment depth. Our findings indicated that the nitrate-reducing bacteria (Acinetobacter, Hydrogenophaga, and Pseudomonas) may be prevalent in the sediment core of Lake Sayram. Canonical correspondence analysis showed that carbonate and total organic carbon (TOC) may be the main environmental factors affecting the vertical patterns of bacterial community composition (BCC) in the sediment of Lake Sayram. This work significantly contributes to our understanding of the BCC of sediments from alpine lakes in arid and semiarid regions.

Photovoltaic panels have altered grassland plant biodiversity and soil microbial diversity

Introduction

Human concerns about fossil fuel depletion, energy security and environmental degradation have driven the rapid development of solar photovoltaic (PV) power generation. Most of the photovoltaic power generation plants are concentrated in desert, grassland and arable land, which means the change of land use type. However, there is still a gap in the research of the PV panel layout on grassland plant species diversity and ecological function.

Methods

In this study, Illumina high-throughput sequencing technology was used to investigate the effects of PV panel arrangement on grassland plant species diversity and soil microbial diversity. In view of the differences in the microclimate at different sites of the PV panels, quadrates were arranged in front edge (FE), beneath the center of each panel (BP), back edge (BE), the uncovered interspace adjacent to each panel (IS) and the undisturbed grassland around the PV panels (Control), respectively.

Results

PV panels (especially FE) significantly increased the total aboveground productivity (total AGB) and plant species diversity in grasslands. FE increased precipitation accumulation and plant species diversity directly and indirectly changed the diversity of soil bacterial and fungal communities. PV panels decreased the relative abundance of Actinobacteriota, while increased the relative abundance of Proteobacteria, Acidobacteriota, and Methylomirabilota. EC, Margalef' s richness and total AGB were the main factors affecting the composition of bacterial communities, while alkaline hydrolysis nitrogen (AN) and available phosphorus (AP) were the main factors affecting the composition of fungal communities.

Discussion

In conclusion, the arrangement of PV panels increased the plant species diversity and soil microorganisms in grassland. This study provides important information for further understanding the impact of PV panels on grassland ecosystem function and is of great significance for maintaining grassland ecosystem function.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale

Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.

White Rann of Kachchh harbours distinct microbial diversity reflecting its unique biogeography

The understanding of sub-surface soil microbial diversity is limited at both saline and hypersaline ecosystems, even though salinity is found to affect the microbial community in aqueous and terrestrial environment. In this study, a phylo-taxonomy analysis as well as the functional characteristics of microbial community of flat salt basin of White Rann of Kachchh (WR), Gujarat, India was performed along the natural salinity gradient. The high throughput sequencing approach has revealed the numerical abundance of bacteria relative to the archaea. Salinity, TOC, EC and sulphate concentration might be the primary driver of the community distribution along the transect at WR. The much anticipated effect of salinity gradient on the microbial composition surprisingly turned out to be more speculative, with little variance in the community composition along the spatial distance of WR. The metabolic pathways involved in energy metabolism (like carbon, nitrogen, sulphur) along with environmental adaptive genes (like osmotic and oxidative stress response, heat and cold shock genes clusters) were abundantly annotated from shot-gun metagenomic study. The carbonic anhydrase harbouring bacteria Bacillus sp. DM4CA1 was isolated from WR, having a catalytic ability for converting the gaseous carbon dioxide in presence of calcium carbonate into calcite at 25 % higher rate as compared to non-harbouring strains. The enzyme has a role in multiple alternative pathways in microbial metabolism. With the array of results obtained, the study could become the new reference for understanding the diversity structure and functional characteristics of the microbial community of terrestrial saline environment.

Linking soil bacterial diversity to satellite-derived vegetation productivity: a case study in arid and semi-arid desert areas

Increasing studies have begun to focus on biodiversity-productivity relationships for soil microorganisms through molecular ecology methods. However, most of these studies involve controlled experiments, and whether the relationship remains at large spatial scales is still largely unknown. To unravel this issue, archived desert soils from long-term experiments were analysed using high-throughput sequencing, and satellite-derived vegetation datasets were acquired to quantify productivity. Most of the abundant genera were significantly different between low- and high-productivity conditions, and soil bacterial communities were strongly impacted by productivity. Soil bacterial biodiversity, including observed operational taxonomic units and the Chao1, Shannon, and Faith's PD indexes, increased rapidly with productivity at low levels and then reached a relatively stable state, and similar phenomena were observed at multiple taxonomic ranks and for most of the dominant groups. Furthermore, we discovered that the mechanisms resulting in the observed relationship might be ecosystem resource availability in large-scale regions and species competition in local regions. Collectively, these results enhance our understanding of the linkage between belowground microorganisms and aboveground vegetation in arid and semi-arid areas and confirm the potential value of satellite-derived datasets in research on soil microbial diversity at large spatial scales.

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

BACKGROUND

Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities.

RESULTS

We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists' community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced.

CONCLUSIONS

We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system. Video Abstract.

Plant Microbiota Beyond Farming Practices: A Review

Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.

The bacterial communities of surface soils from desert sites in the eastern Utah (USA) portion of the Colorado Plateau

Desert-like areas located in the eastern portion of the state of Utah (USA) have geographic features that can resemble the surface of the planet Mars, characterized by red-colored hills, soils and sandstones. We examined the bacterial biodiversity of surface soil samples from several sites from the Colorado Plateau Desert in eastern Utah using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. The sample sites cover the Great Basin, Goblin Valley State Park and nearby regions on the Colorado Plateau. We also examined several physicochemical parameters of the soil samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Proteobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. The most abundant genera in our samples were found to belong to the Cesiribacter, Lysobacter, Adhaeribacter, Microvirga and Pontibacter genera. We found that the relative abundance of Proteobacteria and Gemmatimonadetes were significantly correlated with soil pH and a low concentration of organic matter, suggesting that, in these relatively high-altitude desert soils, these two parameters may be of primary importance to influence bacterial community composition.

Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica

The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.

The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica

The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

Effects of soil preservation for biodiversity monitoring using environmental DNA

Environmental DNA (eDNA) metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa such as soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guideline for best practices so far. Here, we assessed the impact of four methods of soil sample preservation that can be conveniently used also in metabarcoding studies targeting remote or difficult to access areas. Tested methods include: preservation at room temperature for 6 hr, preservation at 4°C for 3 days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6 hr at room temperature and preservation for 21 days. For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under ideal conditions (i.e., extraction of eDNA immediately after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in molecular operational taxonomic units (MOTU) richness of bacteria, fungi and eukaryotes across treatments, but MOTU richness was similar across preservation methods if rare taxa were not considered. All the approaches were able to identify differences in community structure among habitats, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.

Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils

The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical "high-productivity" MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted.

Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding

Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here, we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage. In terms of algal and cyanobacterial biodiversity, the genera Chloromonas, Coccomyxa, Elliptochloris and Nostoc were identified in all samples regardless of origin confirming their ubiquitous distribution. For the first time, we found the chrysophyte Spumella to be common in polar BSCs as it was present in all analyzed samples. Co-occurrence analysis revealed the presence of sulfur metabolizing microbes indicating that BSCs also play an important role for the sulfur cycle. In general, phototrophs were most abundant within the BSCs but there was also a diverse community of heterotrophs and saprotrophs. Our results show that BSCs are unique microecosystems in polar environments with an unexpectedly high biodiversity.

Linking bacterial community composition to soil salinity along environmental gradients

Salinization is recognized as a threat to soil fertility worldwide. A challenge in understanding the effects of salinity on soil microbial communities is the fact that it can be difficult to disentangle the effects of salinity from those of other variables that may co-vary with salinity. Here we use a trait-based approach to identify direct effects of salinity on soil bacterial communities across two salinity gradients. Through dose-response relationships between salinity and bacterial growth, we quantified distributions of the trait salt tolerance within the communities. Community salt tolerance was closely correlated with soil salinity, indicating a strong filtering effect of salinity on the bacterial communities. Accompanying the increases in salt tolerance were consistent shifts in bacterial community composition. We identified specific bacterial taxa that increased in relative abundances with community salt tolerance, which could be used as bioindicators for high community salt tolerance. A strong filtering effect was also observed for pH across the gradients, with pH tolerance of bacterial communities correlated to soil pH. We propose phenotypic trait distributions aggregated at the community level as a useful approach to study the role of environmental factors as filters of microbial community composition.

Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution

Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.

Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages

Imbalances in C:N:P supply ratios may cause bacterial resource limitations and constrain biogeochemical processes, but the importance of shifts in soil stoichiometry are complicated by the nearly limitless interactions between an immensely rich species pool and a multiple chemical resource forms. To more clearly identify the impact of soil C:N:P on bacteria, we evaluated the cumulative effects of single and coupled long-term nutrient additions (i.e., C as mannitol, N as equal concentrations NH4+ and NO3-, and P as Na3PO4) and water on communities in an Antarctic polar desert, Taylor Valley. Untreated soils possessed relatively low bacterial diversity, simplified organic C sources due to the absence of plants, limited inorganic N, and excess soil P potentially attenuating links between C:N:P. After 6 years of adding resources, an alleviation of C and N colimitation allowed one rare Micrococcaceae, an Arthrobacter species, to dominate, comprising 47% of the total community abundance and elevating soil respiration by 136% relative to untreated soils. The addition of N alone reduced C:N ratios, elevated bacterial richness and diversity, and allowed rare taxa relying on ammonium and nitrite for metabolism to become more abundant [e.g., nitrite oxidizing Nitrospira species (Nitrosomonadaceae), denitrifiers utilizing nitrite (Gemmatimonadaceae) and members of Rhodobacteraceae with a high affinity for ammonium]. Based on community co-occurrence networks, lower C:P ratios in soils following P and CP additions created more diffuse and less connected communities by disrupting 73% of species interactions and selecting for taxa potentially exploiting abundant P. Unlike amended nutrients, water additions alone elicited no lasting impact on communities. Our results suggest that as soils become nutrient rich a wide array of outcomes are possible from species dominance and the deconstruction of species interconnectedness to the maintenance of biodiversity.

Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico

Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.

Bacterial community composition in relation to bedrock type and macrobiota in soils from the Sør Rondane Mountains, East Antarctica

Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km(2) Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP-dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.

Microbial Communities in a High Arctic Polar Desert Landscape

The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with β-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with α-diversity, particularly with the Shannon diversity and Chao 1 richness indices.