Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. Here we use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

Differences in soil microbial community structure and assembly processes under warming and cooling conditions in an alpine forest ecosystem

Global climate change affects the soil microbial community assemblages of many ecosystems. However, little is known about the effects of climate warming on the structure of soil microbial communities or the underlying mechanisms that influence microbial community composition in alpine forest ecosystems. Thus, our ability to predict the future consequences of climate change is limited. In this study, with the use of PVC pipes, the in situ soils of the rush-tip long-bud Abies georgei var. smithii forest at 3500 and 4300 m above sea level (MASL) of the Sygera Mountains were incubated in pairs for 1 year to simulate climate cooling and warming. This shift corresponds to a change in soil temperature of ±4.7 °C. Findings showed that climate warming increased the complexity of bacterial networks but decreased the complexity of fungal networks. Climate cooling also increased the complexity of bacterial networks. However, in fungal communities, climate cooling increased the number of nodes but decreased the total number of edges. Stochastic processes acted as the drivers of bacterial community composition, with climate warming leading the shift from deterministic to stochastic drivers. Fungal communities were more sensitive to climate change than bacterial communities, with soil temperature (ST) and soil water content (SWC) acting as the main drivers of change. By contrast, soil bacterial communities were more closely related to soil conditions than fungal communities and remained stable after a year of soil transplantation. In conclusion, fungi and bacteria had different response patterns, and their responses to climate cooling and warming were asymmetric. This work is expected to contribute to our understanding of the response to climate change of soil microbial communities in alpine forests and our prediction of the functions of soil microbial ecosystems in alpine forests.

Elevational characteristics of soil bacterial community and their responses to soil translocation at a mountainside in northwest Sichuan, China

How the soil bacterial communities vary with elevation is context-dependent, and the effect of soil translocation between elevations on bacterial community structure and metabolic function was not fully understood yet. Here, the bacterial community composition and diversity at five elevations along a 1600-3000 m elevation gradient on a mountainside in northwest Sichuan were characterized, and the responses of soil bacterial community to simulated climate changes were further studied by soil translocation reciprocally at three elevations for 12 months. Significant differences were found in soil temperature and moisture at different elevations, but there was no observed change in bacterial alpha diversity. The relative abundance of bacterial phyla was significantly different among the five elevations except for Proteobacteria (the dominant bacterial phyla in five elevation), and most bacterial phyla correlated with soil temperature, moisture, pH and soil bulk density. The direct effect of soil properties (pH, soil nutrients and soil bulk density) on soil bacterial community was stronger than the direct effect of temperature and moisture. Soil translocation changed the relative abundance of some bacterial phyla, and taxonomic groups with significant changes were mainly non-dominant phyla rather than the dominant phyla. Metabolism was the primary function of bacterial community at all elevations, which accounted for ~ 80% of relative abundance, and soil translocation had little effect on metabolic function. These findings indicated that soil bacterial dominant taxa and soil bacterial metabolic functions are relatively stable, which contribute to the stability of the ecosystem when response to the climate change in the future.

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Effect of Co-Application of Azospirillum brasilense and Rhizobium pisi on Wheat Performance and Soil Nutrient Status under Deficit and Partial Root Drying Stress

Water management techniques are improving at the farm level, but they are not enough to deal with the limited availability of water and increased crop yields. Soil microbes play a vital role in nitrogen fixation, improving soil fertility and enhancing plant growth hormones under drought conditions. Therefore, this study was conducted to investigate the impact of water management combined with Azospirillum brasilense and Rhizobium pisi on wheat crop productivity and soil properties in dry regions. Three water management techniques were compared, normal irrigation as a control (C), deficit irrigation (DI), and partial root drying irrigation (PRD), together with the interaction of plant-growth-promoting rhizobacteria (PGPR). Experiments were conducted with six treatments in total: T1 = C + No PGPR, T2 = C + PGPR, T3 = DI + No PGPR, T4 = DI + PGPR, T5 = PRD + No PGPR, and T6 = PRD + PGPR. The highest grain yield was achieved in the control irrigation treatment using seeds inoculated with rhizobacteria, followed by control treatment without any inoculation, and the lowest was recorded with deficit irrigation without rhizobacteria inoculated in the seeds. However, PRD irrigation resulted in significantly higher plant growth and grain yield than the DI treatment. PGPR inoculation combined with PRD resulted in a 22% and 20% higher number of grains per spike, a 19% and 21% higher grain yield, and a 25% and 22% higher crop growth rate compared to rhizobacteria inoculation combined with the DI system in 2021-22 and 2022-23, respectively. This increase was due to the higher production of growth hormones and higher leaf area index under water-limited conditions. A greater leaf area index leads to a higher chlorophyll content and higher food production for plant growth.

Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system

Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.

Vector microbiome: will global climate change affect vector competence and pathogen transmission?

Vector-borne diseases are among the greatest causes of human suffering globally. Several studies have linked climate change and increasing temperature with rises in vector abundance, and in the incidence and geographical distribution of diseases. The microbiome of vectors can have profound effects on how efficiently a vector sustains pathogen development and transmission. Growing evidence indicates that the composition of vectors' gut microbiome might change with shifts in temperature. Nonetheless, due to a lack of studies on vector microbiome turnover under a changing climate, the consequences for vector-borne disease incidence are still unknown. Here, we argue that climate change effects on vector competence are still poorly understood and the expected increase in vector-borne disease transmission might not follow a relationship as simple and straightforward as past research has suggested. Furthermore, we pose questions that are yet to be answered to enhance our current understanding of the effect of climate change on vector microbiomes, competence, and, ultimately, vector-borne diseases transmission.

Soil warming during winter period enhanced soil N and P availability and leaching in alpine grasslands: A transplant study

Alpine meadows are strongly affected by climate change. Increasing air temperature prolongs the growing season and together with changing precipitation patterns alters soil temperature during winter. To estimate the effect of climate change on soil nutrient cycling, we conducted a field experiment. We transferred undisturbed plant-soil mesocosms from two wind-exposed alpine meadows at ~2100 m a.s.l. to more sheltered plots, situated ~300–400 m lower in the same valleys. The annual mean air temperature was 2°C higher at the lower plots and soils that were normally frozen at the original plots throughout winters were warmed to ~0°C due to the insulation provided by continuous snow cover. After two years of exposure, we analyzed the nutrient content in plants, and changes in soil bacterial community, decomposition, mineralization, and nutrient availability. Leaching of N and P from the soils was continuously measured using ion-exchange resin traps. Warming of soils to ~0°C during the winter allowed the microorganisms to remain active, their metabolic processes were not restricted by soil freezing. This change accelerated nutrient cycling, as evidenced by increased soil N and P availability, their higher levels in plants, and elevated leaching. In addition, root exudation and preferential enzymatic mining of P over C increased. However, any significant changes in microbial biomass, bacterial community composition, decomposition rates, and mineralization during the growing season were not observed, suggesting considerable structural and functional resilience of the microbial community. In summary, our data suggest that changes in soil temperature and snow cover duration during winter periods are critical for altering microbially-mediated processes (even at unchanged soil microbial community and biomass) and may enhance nutrient availability in alpine meadows. Consequently, ongoing climate change, which leads to soil warming and decreasing snow insulation, has a potential to significantly alter nutrient cycling in alpine and subalpine meadows compared to the current situation and increase the year-on-year variability in nutrient availability and leaching.

Potential Effects of Biochar Application for Improving Wheat (Triticum aestivum L.) Growth and Soil Biochemical Properties under Drought Stress Conditions

Different soil amendments are applied to improve soil properties and to achieve higher crop yield under drought conditions. The objective of the study was to investigate the role of biochar for the improvement of wheat (Triticum aestivum L.) growth and soil biochemical properties under drought conditions. A pot experiment with a completely randomized design was arranged with four replications in a wire house. Drought was imposed on two critical growth stages (tillering and grain filling) and biochar was applied to the soil 10 days before sowing at two different rates (28 g kg−1 and 38 g kg−1). Soil samples were collected to determine the soil properties including soil respiration and enzymatic parameters after crop harvesting. Results showed that water stress negatively affects all biochemical properties of the soil, while biochar amendments positively improved these properties. Application of biochar at 38 g kg−1 provided significantly higher mineral nutrients, Bray P (18.72%), exchangeable-K (7.44%), soil carbon (11.86%), nitrogen mineralization (16.35%), and soil respiration (6.37%) as a result of increased microbial activities in comparison with the 28 g kg−1 rate.

Warming-driven migration of core microbiota indicates soil property changes at continental scale

Terrestrial species are predicted to migrate northward under global warming conditions, yet little is known about the direction and magnitude of change in microbial distribution patterns. In this continental-scale study with more than 1600 forest soil samples, we verify the existence of core microbiota and lump them into a manageable number of eco-clusters based on microbial habitat preferences. By projecting the abundance differences of eco-clusters between future and current climatic conditions, we observed the potential warming-driven migration of the core microbiota under warming, partially verified by a field warming experiment at Southwest China. Specifically, the species that favor low pH are potentially expanding and moving northward to medium-latitudes (25°-45°N), potentially implying that warm temperate forest would be under threat of soil acidification with warming. The eco-cluster of high-pH with high-annual mean temperature (AMT) experienced significant abundance increases at middle- (35°-45°N) to high-latitudes (> 45°N), especially under Representative Concentration Pathway (RCP) 8.5, likely resulting in northward expansion. Furthermore, the eco-cluster that favors low-soil organic carbon (SOC) was projected to increase under warming scenarios at low-latitudes (< 25°N), potentially an indicator of SOC storage accumulation in warmer areas. Meanwhile, at high-latitudes (> 45°N) the changes in relative abundance of this eco-cluster is inversely related with the temperature variation trends, suggesting microbes-mediated soil organic carbon changes are more responsive to temperature variation in colder areas. These results have vital implications for the migration direction of microbial communities and its potential ecological consequences in future warming scenarios.

Changes in Soil Microbial Communities across an Urbanization Gradient: A Local-Scale Temporal Study in the Arid Southwestern USA

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.

Soil quality parameters vis-a-vis growth and yield attributes of sugarcane as influenced by integration of microbial consortium with NPK fertilizers

Intensive agriculture involving high crop intensity, unavailability of organics, and higher use of straight fertilizers causes imbalanced use and deficiencies of several other macro and micronutrients. Nutrients supply through the integration of microbial consortium containing Gluconacetobater diazotrophicus, Trichoderma harzianum, and Pseudomonas fluorescens can reduce the requirements on the one hand and can also increase the response of chemical fertilizers. Thus we had planned the present experiment with the objectives (i) to determine the effect of integrated application of microbial consortium (MC) and NPK fertilizer on soil quality parameters and crop growth and yield attributes and (ii) to assess the effect of integration on agronomic efficiency of N, P and K and find out the possibilities for reduction in applied doses of NPK, if any. Five treatments viz., T₁; N₀P₀K₀; T₂: N₇₅P₁₃K₂₅; T₃: N₁₅₀P₂₆K₅₀; T₄: N₇₅P₁₃K₂₅ + microbial consortium and T₅: N₁₅₀P₂₆K₅₀ + microbial consortium containing new strains of Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens (CFU 10^9–10 per ml liquid culture) were evaluated under four replications in a randomized block design (RBD). Experimental results indicated that integrating microbial consortium and NPK fertilizers' application proved effective in improving soil organic carbon, soil microbial population, microbial biomass carbon, microbial biomass nitrogen, and soil respiration. Integrated use of microbial consortium with NPK also improved the cation exchange capacity of soil and roots. However, the growth and yield attributes, nutrients uptake, sugarcane, and sugar yields also revealed a positive effect of microbial consortium's integrated application with NPK. The integration of MC and NPK also improved the agronomic efficiency of applied nutrients (NPK). Reduction of 50% NPK with these microbial consortia (Trichoderma harzianum, Gluconcetobacter diazotrophicus, and Pseudomonas fluorescens) was found better than the application of full NPK through chemical fertilizers. Thus application of N₁₅₀P₂₆K₅₀ with microbial consortium can sustain soil fertility besides improving sugarcane and sugar yields in subtropical Indian conditions.

Contrasting responses of above- and below-ground herbivore communities along elevation

Above- and below-ground herbivory are key ecosystem processes that can be substantially altered by environmental changes. However, direct comparisons of the coupled variations of above- and below-ground herbivore communities along elevation gradients remain sparse. Here, we studied the variation in assemblages of two dominant groups of herbivores, namely, aboveground orthoptera and belowground nematodes, in grasslands along six elevation gradients in the Swiss Alps. By examining variations of community properties of herbivores and their food plants along montane clines, we sought to determine whether the structure and functional properties of these taxonomic groups change with elevation. We found that orthoptera decreased in both species richness and abundance with elevation. In contrast with aboveground herbivores, the taxonomic richness and the total abundance of nematode did not covary with elevation. We further found a stronger shift in above- than below-ground functional properties along elevation, where the mandibular strength of orthoptera matched a shift in leaf toughness. Nematodes showed a weaker pattern of declined sedentary behavior and increased mobility with elevation. In contrast to the direct exposal of aboveground organisms to the surface climate, conditions may be buffered belowground, which together with the influence of edaphic factors on the biodiversity of soil biota, may explain the differences between elevational patterns of above- and below-ground communities. Our study emphasizes the necessity to consider both the above- and below-ground compartments to understand the impact of current and future climatic variation on ecosystems, from a functional perspective of species interactions.

Historical Drought Affects Microbial Population Dynamics and Activity During Soil Drying and Re-Wet

A history of drought exposure promoted by variable precipitation regimes can select for drought-tolerant soil microbial taxa, but the mechanisms of survival and death of microbial populations through the selective stresses of soil drying and re-wet are not well understood. We subjected soils collected from a 15-year field drought experiment ("Altered" precipitation history with extended dry periods, versus the "Ambient" field control) to a laboratory drying/re-wetting experiment, to learn whether selective population survival, death, or maintenance of protein synthesis potential and microbial respiration through variable soil water conditions was affected by field drought legacy. Microbial community composition, as measured by Illumina MiSeq sequencing of the 16S rRNA and 16S rRNA gene, shifted with laboratory drying/re-wet and field drought treatments. In Ambient soils, there was a higher proportion of reduced OTU abundance (indicative of mortality) during re-wet, whereas Altered soils had a greater proportion of stable OTU populations that did not change in abundance (indicative of survival) through drying/re-wet. Altered soils also had a lower proportion of rRNA:rRNA genes (lower protein synthesis potential) during dry-down, a greater weighted mean rRNA operon number (potential growth rate and r-selection) which was associated with higher abundance of Firmicutes (order Bacillales), and lower average microbial respiration rates. These data demonstrate that soils with a weaker historical drought legacy exhibit a higher prevalence of microbial water-stress mortality and differential survival and death at OTU levels following short-term dryingand re-wetting, concurrent with higher carbon loss potential. This work provides novel insight into the mechanisms and consequences of soil microbial changes resulting from extended drought conditions.

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

Integrating Computational Methods to Investigate the Macroecology of Microbiomes

Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.

The global soil community and its influence on biogeochemistry

Soil organisms represent the most biologically diverse community on land and govern the turnover of the largest organic matter pool in the terrestrial biosphere. The highly complex nature of these communities at local scales has traditionally obscured efforts to identify unifying patterns in global soil biodiversity and biogeochemistry. As a result, environmental covariates have generally been used as a proxy to represent the variation in soil community activity in global biogeochemical models. Yet over the past decade, broad-scale studies have begun to see past this local heterogeneity to identify unifying patterns in the biomass, diversity, and composition of certain soil groups across the globe. These unifying patterns provide new insights into the fundamental distribution and dynamics of organic matter on land.

Ecological mechanisms underlying soil bacterial responses to rainfall along a steep natural precipitation gradient

Changes in the structure and function of soil microbial communities can drive substantial ecosystem feedbacks to altered precipitation. However, the ecological mechanisms underlying community responses to environmental change are not well understood. We used an 18-month soil reciprocal transplant experiment along a steep precipitation gradient to quantify how changes in rainfall affected bacterial community structure. We also conducted an enhanced dispersal treatment to ask whether higher immigration rates of taxa from the surrounding environment would accelerate community responses to climate change. Finally, we addressed how the composition of soil bacteria communities was related to the functional response of soil respiration to moisture in these treatments. Bacterial community structure (OTU abundance) and function (respiration rates) changed little in response to manipulation of either rainfall environment or dispersal rates. Although most bacteria were ecological generalists, a subset of specialist taxa, over 40% of which were Actinobacteria, tended to be more abundant in the rainfall environment that matched their original conditions. Bacteria community composition was an important predictor of the respiration response to moisture. Thus, the high compositional resistance of microbial communities dictated respiration responses to altered rainfall in this system.

Novel microbial community composition and carbon biogeochemistry emerge over time following saltwater intrusion in wetlands

Sea level rise and changes in precipitation can cause saltwater intrusion into historically freshwater wetlands, leading to shifts in microbial metabolism that alter greenhouse gas emissions and soil carbon sequestration. Saltwater intrusion modifies soil physicochemistry and can immediately affect microbial metabolism, but further alterations to biogeochemical processing can occur over time as microbial communities adapt to the changed environmental conditions. To assess temporal changes in microbial community composition and biogeochemical activity due to saltwater intrusion, soil cores were transplanted from a tidal freshwater marsh to a downstream mesohaline marsh and periodically sampled over 1 year. This experimental saltwater intrusion produced immediate changes in carbon mineralization rates, whereas shifts in the community composition developed more gradually. Salinity affected the composition of the prokaryotic community but did not exert a strong influence on the community composition of fungi. After only 1 week of saltwater exposure, carbon dioxide production doubled and methane production decreased by three orders of magnitude. By 1 month, carbon dioxide production in the transplant was comparable to the saltwater controls. Over time, we observed a partial recovery in methane production which strongly correlated with an increase in the relative abundance of three orders of hydrogenotrophic methanogens. Taken together, our results suggest that ecosystem responses to saltwater intrusion are dynamic over time as complex interactions develop between microbial communities and the soil organic carbon pool. The gradual changes in microbial community structure we observed suggest that previously freshwater wetlands may not experience an equilibration of ecosystem function until long after initial saltwater intrusion. Our results suggest that during this transitional period, likely lasting years to decades, these ecosystems may exhibit enhanced greenhouse gas production through greater soil respiration and continued methanogenesis.

Effect of climate change on humic substances and associated impacts on the quality of surface water and groundwater: A review

Humic substances (HS), a highly transformed part of non-living natural organic matter (NOM), comprise up to 70% of the soil organic matter (SOM), 50-80% of dissolved organic matter (DOM) in surface water, and 25% of DOM in groundwater. They considerably contribute to climate change (CC) by generating greenhouse gases (GHG). On the other hand, CC affects HS, their structure and reactivity. HS important role in global warming has been recognized and extensively studied. However, much less attention has been paid so far to effects on the freshwater quality, which may result from the climate induced impact on HS, and HS interactions with contaminants in soil, surface water and groundwater. It is expected that an increased temperature and enhanced biodegradation of SOM will lead to an increase in the production of DOM, while the flooding and runoff will export it from soil to rivers, lakes, and groundwater. Microbial growth will be stimulated and biodegradation of pollutants in water can be enhanced. However, there may be also negative effects, including an inhibition of solar disinfection in brown lakes. The CC induced desorption from soil and sediments, as well as re-mobilization of metals and organic pollutants are anticipated. In-situ treatment of surface water and groundwater may be affected. Quality of the source freshwater is expected to deteriorate and drinking water production may become more expensive. Many of the possible effects of CC described in this article have yet to be explored and understood. Enormous potential for interesting, multidisciplinary studies in the important research areas has been presented.

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010-2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P < 0.05) increased root and microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P < 0.05) changed by clipping. Clipping significantly (P < 0.05) increased the abundances of labile carbon (C) degrading genes. More importantly, the abundances of recalcitrant C degrading genes were consistently and significantly (P < 0.05) increased by clipping in the last 2 years, which could accelerate recalcitrant C degradation and weaken long-term soil carbon stability. Furthermore, genes involved in nutrient-cycling processes including nitrogen cycling and phosphorus utilization were also significantly increased by clipping. The shifts of microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices.

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient

Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature.

Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades

Measurements of carbon isotope contents of plant organic matter provide important information in diverse fields such as plant breeding, ecophysiology, biogeochemistry and paleoclimatology. They are currently based on ¹³C/¹²C ratios of specific, whole metabolites, but we show here that intramolecular ratios provide higher resolution information. In the glucose units of tree-ring cellulose of 12 tree species, we detected large differences in ¹³C/¹²C ratios (>10‰) among carbon atoms, which provide isotopically distinct inputs to major global C pools, including wood and soil organic matter. Thus, considering position-specific differences can improve characterisation of soil-to-atmosphere carbon fluxes and soil metabolism. In a Pinus nigra tree-ring archive formed from 1961 to 1995, we found novel ¹³C signals, and show that intramolecular analysis enables more comprehensive and precise signal extraction from tree rings, and thus higher resolution reconstruction of plants’ responses to climate change. Moreover, we propose an ecophysiological mechanism for the introduction of a ¹³C signal, which links an environmental shift to the triggered metabolic shift and its intramolecular ¹³C signature. In conclusion, intramolecular ¹³C analyses can provide valuable new information about long-term metabolic dynamics for numerous applications.

Reef-Building Corals as a Tool for Climate Change Research in the Genomics Era

Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.

Historical climate controls soil respiration responses to current soil moisture

Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40-70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration-moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall.

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

Extracellular DNA from dead microorganisms can persist in soil for weeks to years^1-3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide⁴. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.