Minor Changes in Soil Bacterial and Fungal Community Composition Occur in Response to Monsoon Precipitation in a Semiarid Grassland

Arizona and New Mexico receive half of their annual precipitation during the summer monsoon season, making this large-scale rain event critical for ecosystem productivity. We used the monsoon rains to explore the responses of soil bacterial and fungal communities to natural moisture pulses in a semiarid grassland. Through 454 pyrosequencing of the 16S rRNA gene and ITS region, we phylogenetically characterized these communities at 22 time points during a summer season. Relative humidity increased before the rains arrived, creating conditions in soil that allowed for the growth of microorganisms. During the course of the study, the relative abundances of most bacterial phyla showed little variation, though some bacterial populations responded immediately to an increase in soil moisture once the monsoon rains arrived. The Firmicutes phylum experienced over a sixfold increase in relative abundance with increasing water availability. Conversely, Actinobacteria, the dominant taxa at our site, were negatively affected by the increase in water availability. No relationship was found between bacterial diversity and soil water potential. Bacterial community structure was unrelated to all environmental variables that we measured, with the exception of a significant relationship with atmospheric relative humidity. Relative abundances of fungal phyla fluctuated more throughout the season than bacterial abundances did. Variation in fungal community structure was unrelated to soil water potential and to most environmental variables. However, ordination analysis showed a distinct fungal community structure late in the season, probably due to plant senescence.     

Soil Microbial Community Response to Drought and Precipitation Variability in the Chihuahuan Desert

Increases in the magnitude and variability of precipitation events have been predicted for the Chihuahuan Desert region of West Texas. As patterns of moisture inputs and amounts change, soil microbial communities will respond to these alterations in soil moisture windows. In this study, we examined the soil microbial community structure within three vegetation zones along the Pine Canyon Watershed, an elevation and vegetation gradient in Big Bend National Park, Chihuahuan Desert. Soil samples at each site were obtained in mid-winter (January) and in mid-summer (August) for 2 years to capture a component of the variability in soil temperature and moisture that can occur seasonally and between years along this watershed. Precipitation patterns and amounts differed substantially between years with a drought characterizing most of the second year. Soils were collected during the drought period and following a large rainfall event and compared to soil samples collected during a relatively average season. Structural changes within microbial community in response to site, season, and precipitation patterns were evaluated using fatty acid methyl ester (FAME) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses. Fungal FAME amounts differed significantly across seasons and sites and greatly outweighed the quantity of bacterial and actinomycete FAME levels for all sites and seasons. The highest fungal FAME levels were obtained in the low desert scrub site and not from the high elevation oak–pine forests. Total bacterial and actinomycete FAME levels did not differ significantly across season and year within any of the three locations along the watershed. Total bacterial and actinomycete FAME levels in the low elevation desert-shrub and grassland sites were slightly higher in the winter than in the summer. Microbial community structure at the high elevation oak–pine forest site was strongly correlated with levels of NH₄ ⁺–N, % soil moisture, and amounts of soil organic matter irrespective of season. Microbial community structure at the low elevation desert scrub and sotol grasslands sites was most strongly related to soil pH with bacterial and actinobacterial FAME levels accounting for site differences along the gradient. DGGE band counts of amplified soil bacterial DNA were found to differ significantly across sites and season with the highest band counts found in the mid-elevation grassland site. The least number of bands was observed in the high elevation oak–pine forest following the large summer-rain event that occurred after a prolonged drought. Microbial responses to changes in precipitation frequency and amount due to climate change will differ among vegetation zones along this Chihuahuan Desert watershed gradient. Soil bacterial communities at the mid-elevation grasslands site are the most vulnerable to changes in precipitation frequency and timing, while fungal community structure is most vulnerable in the low desert scrub site. The differential susceptibility of the microbial communities to changes in precipitation amounts along the elevation gradient reflects the interactive effects of the soil moisture window duration following a precipitation event and differences in soil heat loads. Amounts and types of carbon inputs may not be as important in regulating microbial structure among vegetation zones within in an arid environment as is the seasonal pattern of soil moisture and the soil heat load profile that characterizes the location.     

Soil Microbial Community Response to Nitrobenzene Exposure for a Spartina Wetland

To explore the response of the soil microbial community to nitrobenzene (NB) exposure in a Spartina marsh, a short-term (45 d) mesocosm study was conducted at three NB concentrations of (10, 50, and 100) mg kg^?1. Dry soil, sterile and unsterile controls were also compared. The ability of the microbes to biodegrade NB was studied in an effort to predict the outcome of NB in the mesocosm. The results indicated that a microbial community is capable of doing so. Microbial enumeration and enzyme assays showed that the fluctuations in microbial communities and polyphenol oxidase activities are related to the initial NB concentration. Moreover, cluster analyses through denaturing gradient gel electrophoresis (DGGE) revealed very similar patterns (95.5%) throughout the 45 d term, indicating that the microbial community regenerates when NB is exhausted. Although volatilization and photolysis were the major processes responsible for the reduction in NB in contaminated mesocosms and the microbial community regenerated at the end of incubation, the data indicate potential ecological risks in outfall areas even if the discharged wastewater complies with the national wastewater discharge standards.     

Burning Fire-Prone Mediterranean Shrublands: Immediate Changes in Soil Microbial Community Structure and Ecosystem Functions

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.     

Biological Soil Crust Microsites Are the Main Contributor to Soil Respiration in a Semiarid Ecosystem

Biological soil crusts (BSCs) are a key biotic component of dryland ecosystems worldwide. However, most studies carried out to date on carbon (C) fluxes in these ecosystems, such as soil respiration, have neglected them. We conducted a 3.5-year field experiment to evaluate the spatio-temporal heterogeneity of soil respiration in a semiarid Stipa tenacissima steppe and to assess the contribution of BSC-dominated areas to the annual soil respiration of the whole ecosystem. We selected the six most frequent microsites in the study area: Stipa tussocks (ST), Retama sphaerocarpa shrubs (RS), and open areas with very low (<5% BSC cover, BS), low, medium and high cover of well-developed BSCs. Soil respiration rates did not differ among BSC-dominated microsites but were significantly higher and lower than those found in BS and ST microsites, respectively. A model using soil temperature and soil moisture accounted for over 85% of the temporal variation in soil respiration throughout the studied period. Using this model, we estimated a range of 240.4–322.6 g C m⁻² y⁻¹ released by soil respiration at our study area. Vegetated (ST and RS) and BSC-dominated microsites accounted for 37 and 42% of this amount, respectively. Our results indicate that accounting for the spatial heterogeneity in soil respiration induced by BSCs is crucial to provide accurate estimations of this flux at the ecosystem level. They also highlight that BSC-dominated areas are the main contributor to the total C released by soil respiration and, therefore, must be considered when estimating C budgets in drylands.     

Response of Microbial Community Composition and Function to Soil Climate Change

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak–grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying ¹³C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their “life history” envelopes.     

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis

The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0–3 m) in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer), PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer). Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0–0.2 m), e.g., Cyanobacteria (25% total abundance) were most abundant in desert soil, while Actinobacteria (26%) were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria) decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales), nitrifying (e.g., Nitrospirae), and anaerobic bacteria (e.g., Anaerolineae) increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis.     

Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.     

Functional Response of a Near-Surface Soil Microbial Community to a Simulated Underground CO2 Storage Leak

Understanding the impacts of leaks from geologic carbon sequestration, also known as carbon capture and storage, is key to developing effective strategies for carbon dioxide (CO₂) emissions management and mitigation of potential negative effects. Here, we provide the first report on the potential effects of leaks from carbon capture and storage sites on microbial functional groups in surface and near-surface soils. Using a simulated subsurface CO₂ storage leak scenario, we demonstrate how CO₂ flow upward through the soil column altered both the abundance (DNA) and activity (mRNA) of microbial functional groups mediating carbon and nitrogen transformations. These microbial responses were found to be seasonally dependent and correlated to shifts in atmospheric conditions. While both DNA and mRNA levels were affected by elevated CO₂, they did not react equally, suggesting two separate mechanisms for soil microbial community response to high CO₂ levels. The results did not always agree with previous studies on elevated atmospheric (rather than subsurface) CO₂ using FACE (Free-Air CO₂ Enrichment) systems, suggesting that microbial community response to CO₂ seepage from the subsurface might differ from its response to atmospheric CO₂ increases.     

Microbial Nonlinear Response to a Precipitation Gradient in the Northeastern Tibetan Plateau

The response of soil microbes to global warming, especially their response to precipitation, remains poorly known. The Tibetan Plateau is very sensitive to climate change. In particular, the northeastern margin of the Tibetan Plateau is an interesting area to test the response of soil microbial communities to precipitation, as there is a distinct gradient in annual precipitation from east to west. We collected soil samples along a precipitation gradient in arid and semi-arid areas of the northeastern Tibetan Plateau. Phospholipid fatty acid (PLFA) technology was used to analyze the microbial community structure and total microbial biomass. With declining precipitation, bacterial biomass decreased significantly, whereas fungal biomass did not show an obvious trend; this result indicates that bacteria are more sensitive to mean annual precipitation (MAP). Overall, the biomass of Gram-negative (G^?) bacteria represented up to 82% of the total bacterial biomass. In the high (260–394 mm yr^?1) MAP areas, bacterial biomass was mainly concentrated at the surface and decreased with increasing soil depth (0–40 cm). In contrast, in the low (36–260 mm yr^?1) MAP areas, bacterial biomass was mainly concentrated in the deep soils. The mean annual precipitation was strongly correlated with soil microbial community in space, with microbial communities in the 0–10-cm soil depth most affected by precipitation. Groundwater may impact microbial communities in the 20–40-cm soil depth of this arid and semiarid region. The clustering of the microbial communities was significantly grouped according to the MAP gradient, revealing that MAP is a major driving force of microbial communities in this arid and semi-arid area. The decline in MAP led to a shift in the structure of the microbial community and an overall reduction in microbial biomass.     

Temporal Asynchrony in Soil Nutrient Dynamics and Plant Production in a Semiarid Ecosystem

A central goal of ecosystem ecology is to understand how the cycling of nutrients and the growth of organisms are linked. Ecologists have repeatedly observed that nutrient mineralization and plant production are closely coupled in time in many terrestrial ecosystems. Typically, mineralization rates of limiting nutrients, particularly of nitrogen, during the growing season determine nutrient availability while pools of mineral nutrients remain low and relatively constant. Although several previous reports suggest nitrogen mineralization has the potential to vary seasonally and out of phase with plant production, such a phenomenon has been poorly documented. Here we report results from a semiarid savanna ecosystem characterized by distinct temporal asynchrony in rates of soil nitrogen cycling and plant production. Periods of positive plant growth following the onset of rains coincide with periods of low N turnover rates, whereas higher rates occur late in the wet season following plant senescence and throughout dry seasons. Plant uptake from the substantial mineral N pool present early in the growing season is sufficient to explain most of the N allocation to aboveground plant biomass during the growing season, even in the absence of any wet-season mineralization. The mineral N pool is subsequently recharged by late wet- and dry-season mineralization, plus urine inputs at sites with high levels of ungulate activity. These findings suggest fundamental changes in the quality of substrates available to decomposers over a seasonal cycle, with significant implications for the partitioning of limiting nutrients by plant species, the seasonal pattern of nutrient limitations of aboveground production, and the effective use of N fertilizers in semiarid ecosystems.     

Response of the Abundance of Key Soil Microbial Nitrogen-Cycling Genes to Multi-Factorial Global Changes

Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.     

Shifting Species Interaction in Soil Microbial Community and Its Influence on Ecosystem Functions Modulating

The supportive and negative evidence for the stress gradient hypothesis (SGH) led to an ongoing debate among ecologists and called for new empirical and theoretical work. In this study, we took various biological soil crust (BSCs) samples along a spatial gradient with four environmental stress levels to examine the fitness of SGH in microbial interactions and evaluate its influence on biodiversity–function relationships in BSCs. A new assessment method of species interactions within hard-cultured invisible soil community was employed, directly based on denaturing gradient gel electrophoresis fingerprint images. The results showed that biotic interactions in soil phototroph community dramatically shifted from facilitation to dominant competition with the improvement of microhabitats. It offered new evidence, which presented a different perspective on the hypothesis that the relative importance of facilitation and competition varies inversely along the gradient of abiotic stress. The path analysis indicated that influence of biotic interactions (r?=?0.19, p?<?0.05) on ecosystem functions is lower than other community properties (r?=?0.62, p?<?0.001), including soil moisture, crust coverage, and biodiversity. Furthermore, the correlation between species interactions and community properties was non-significant with low negative influence (r?=??0.27, p?>?0.05). We demonstrate that the inversion of biotic interaction as a response to the gradient of abiotic stresses existed not only in the visible plant community but also in the soil microbial community.     

Using Real-Time PCR to Assess Changes in the Hydrocarbon-Degrading Microbial Community in Antarctic Soil During Bioremediation

A real-time polymerase chain reaction (PCR) method to quantify the proportion of microorganisms containing alkane monooxygenase was developed and used to follow changes in the microbial community in hydrocarbon-contaminated Antarctic soil during a bioremediation field trial. Assays for the alkB and rpoB genes were validated and found to be both sensitive and reproducible (less than 2% intrarun variation and 25–38% interrun variation). Results from the real-time PCR analysis were compared to analysis of the microbial population by a culture-based technique [most probable number (MPN) counts]. Both types of analysis indicated that fertilizer addition to hydrocarbon-contaminated soil stimulated the indigenous bacterial population within 1 year. The proportion of alkB containing microorganisms was positively correlated to the concentration of n-alkanes in the soil. After the concentration of n-alkanes in the soil decreased, the proportion of alkane-degrading microorganisms decreased, but the proportion of total hydrocarbon-degrading microorganisms increased, indicating another shift in the microbial community structure and ongoing biodegradation.     

Soil Microbial Community Response to Land Use Change in an Agricultural Landscape of Western Kenya

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.     

Response of Estuarine Biofilm Microbial Community Development to Changes in Dissolved Oxygen and Nutrient Concentrations

The information content and responsiveness of microbial biofilm community structure, as an integrative indicator of water quality, was assessed against short-term changes in oxygen and nutrient loading in an open-water estuarine setting. Biofilms were grown for 7-day periods on artificial substrates in the Pensacola Bay estuary, Florida, in the vicinity of a wastewater treatment plant (WWTP) outfall and a nearby reference site. Substrates were deployed floating at the surface and near the benthos in 5.4 m of water. Three sampling events covered a 1-month period coincident with declining seasonal WWTP flow and increasing dissolved oxygen (DO) levels in the bottom waters. Biomass accumulation in benthic biofilms appeared to be controlled by oxygen rather than nutrients. The overriding effect of DO was also seen in DNA fingerprints of community structure by terminal restriction fragment length polymorphism (T-RFLP) of amplified 16S rRNA genes. Ribotype diversity in benthic biofilms at both sites dramatically increased during the transition from hypoxic to normoxic. Terminal restriction fragment length polymorphism patterns showed pronounced differences between benthic and surface biofilm communities from the same site in terms of signal type, strength, and diversity, but minor differences between sites. Sequencing of 16S rRNA gene clone libraries from benthic biofilms at the WWTP site suggested that low DO levels favored sulfate-reducing prokaryotes (SRP), which decreased with rising oxygen levels and increasing overall diversity. A 91-bp ribotype in the CfoI-restricted 16S rRNA gene T-RFLP profiles, indicative of SRP, tracked the decrease in relative SRP abundance over time.     

Microbial Community Changes in a Perturbed Agricultural Soil Investigated by Molecular and Physiological Approaches

Changes in soil microbial activity and diversity after incubation either with nitrogen or with a mixture of methane and air were examined. The perturbation by methane and air were characterized in detail and led to reduced diversity and enrichment of methanotrophs which were identified by denaturing gradient gel electrophoresis and 16S rRNA sequencing.