The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

Although ammonia-oxidizing bacteria (AOB) are likely to play a key role in the soil nitrogen cycle, we have only a limited understanding of how the diversity and composition of soil AOB communities change across ecosystem types. We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suite of environmental variables measured, we found the strongest correlation between temperature and AOB community composition; soils exposed to similar mean annual temperatures tended to have similar AOB communities. This finding is consistent with previous studies and suggests that temperature selects for specific AOB lineages. Given that distinct AOB taxa are likely to have unique functional attributes, the biogeographical patterns exhibited by soil AOB may be directly relevant to understanding soil nitrogen dynamics under changing environmental conditions.     

Spatial Organization of Microbial Biofilm Communities

Abstract The application of advanced microscopy and molecular and electrochemical high-resolution methods has provided insights into the structural organization and function of biofilm communities. It appears that cellular properties such as growth differentiation, chemotaxis, and cell-to-cell signaling enable biofilm communities to organize structurally in response to the external conditions and the activities of the different biofilm members. Thereby resource utilization becomes optimized, and processes which require syntrophic relationships or special micro-environments become facilitated. Received: 23 February 2000; Accepted: 8 June 2000; Online Publication: 28 August 2000     

Soil Microbial Communities of Eastern Antarctica

Investigation of microbial communities of Antarctica soils is a very important field of research that expands our knowledge of microbial participation in primary soil formation and specific features of their communities in extreme habitats, and it is of considerable interest in directed search of for microorganisms as potential biotechnological objects. The results of long-term (2012–2017) complex studies on soil microbial communities of the Russian East Antarctica polar stations at Shirmakher oasis (Novolazarevskaya station), the Larsemann Hills (Progress station), and the Tala Hills (Molodezhnaya station) are presented in this review. The assessment of biomass of soil microorganisms by the methods of direct microscopy has been carried out for the first time for this region. The general amount of microbial biomass is small; the fungi dominate (77–99%). The unique features of Antarctic soils are the high content and morphological diversity of small forms of microorganisms: fungi are presented by mainly single-celled structures (small spores and yeasts), while bacteria by ultrafine (filtering) forms. At the same time, microorganisms can significantly contribute to such important ecological functions of soil as the emission of greenhouse gases, especially during the warm season with the stable positive temperatures of the soil. This should be considered during creation of models and forecasts of global warming. The use of various isolation techniques for the analysis of the soil microbial population, together with the succession approach, significantly expand the information about taxonomic diversity of cultivated fungi and bacteria in Antarctica soils.     

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

Soil microbial communities play a critical role in nutrient transformation and storage in all ecosystems. Quantifying the seasonal and long-term temporal extent of genetic and functional variation of soil microorganisms in response to biotic and abiotic changes within and across ecosystems will inform our understanding of the effect of climate change on these processes. We examined spatial and seasonal variation in microbial communities based on 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) composition across four biomes: a tropical broadleaf forest (Hawaii), taiga (Alaska), semiarid grassland-shrubland (Utah), and a subtropical coniferous forest (Florida). In this study, we used a team-based instructional approach leveraging the iPlant Collaborative to examine publicly available National Ecological Observatory Network (NEON) 16S gene and PLFA measurements that quantify microbial diversity, composition, and growth. Both profiling techniques revealed that microbial communities grouped strongly by ecosystem and were predominately influenced by three edaphic factors: pH, soil water content, and cation exchange capacity. Temporal variability of microbial communities differed by profiling technique; 16S-based community measurements showed significant temporal variability only in the subtropical coniferous forest communities, specifically through changes within subgroups of Acidobacteria. Conversely, PLFA-based community measurements showed seasonal shifts in taiga and tropical broadleaf forest systems. These differences may be due to the premise that 16S-based measurements are predominantly influenced by large shifts in the abiotic soil environment, while PLFA-based analyses reflect the metabolically active fraction of the microbial community, which is more sensitive to local disturbances and biotic interactions. To address the technical issue of the response of soil microbial communities to sample storage temperature, we compared 16S-based community structure in soils stored at -80°C and -20°C and found no significant differences in community composition based on storage temperature. Free, open access datasets and data sharing platforms are powerful tools for integrating research and teaching in undergraduate and graduate student classrooms. They are a valuable resource for fostering interdisciplinary collaborations, testing ecological theory, model development and validation, and generating novel hypotheses. Training in data analysis and interpretation of large datasets in university classrooms through project-based learning improves the learning experience for students and enables their use of these significant resources throughout their careers.     

Oxygen and the Spatial Structure of Microbial Communities

Oxygen has two faces. On one side it is the terminal electron acceptor of aerobic respiration – the most efficient engine of energy metabolism. On the other hand, oxygen is toxic because the reduction of molecular O₂ creates reactive oxygen species such as the superoxide anion, peroxide, and the hydroxyl radical. Probably most prokaryotes, and virtually all eukaryotes, depend on oxygen respiration, and we show that the ambiguous relation to oxygen is both an evolutionary force and a dominating factor driving functional interactions and the spatial structure of microbial communities.We focus on microbial communities that are specialised for life in concentration gradients of oxygen, where they acquire the full panoply of specific requirements from limited ranges of PO₂ , which also support the spatial organisation of microbial communities. Marine and lake sediments provide examples of steep O₂ gradients, which arise because consumption or production of oxygen exceeds transport rates of molecular diffusion. Deep lakes undergo thermal stratification in warm waters, resulting in seasonal anaerobiosis below the thermocline, and lakes with a permanent pycnocline often have permanent anoxic deep water. The oxycline is here biologically similar to sediments, and it harbours similar microbial biota, the main difference being the spatial scale. In sediments, transport is dominated by molecular diffusion, and in the water column, turbulent mixing dominates vertical transport.Cell size determines the minimum requirement of aerobic organisms. For bacteria (and mitochondria), the half‐saturation constant for oxygen uptake ranges within 0.05 – 0.1% atmospheric saturation; for the amoeba Acanthamoeba castellanii it is 0.2%, and for two ciliate species measuring around 150 μm, it is 1‐2 % atmospheric saturation. Protection against O₂ toxicity has an energetic cost that increases with increasing ambient O₂ tension. Oxygen sensing seems universal in aquatic organisms. Many aspects of oxygen sensing are incompletely understood, but the mechanisms seem to be evolutionarily conserved. A simple method of studying oxygen preference in microbes is to identify the preferred oxygen tension accumulating in O₂ gradients. Microorganisms cannot sense the direction of a chemical gradient directly, so they use other devices to orient themselves. Different mechanisms in different prokaryotic and eukaryotic microbes are described. In O₂ gradients, many bacteria and protozoa are vertically distributed according to oxygen tension and they show a very limited range of preferred PO₂. In some pigmented protists the required PO₂ is contingent on light due to photochemically generated reactive oxygen species. In protists that harbour endosymbiotic phototrophs, orientation towards light is mediated through the oxygen production of their photosynthetic symbionts. Oxygen plays a similar role for the distribution of small metazoans (meiofauna) in sediments, but there is little experimental evidence for this. Thus the oxygenated sediments surrounding ventilated animal burrows provide a special habitat for metazoan meiofauna as well as unicellular organisms.     

Mineral Type Structures Soil Microbial Communities

Soil microorganisms living in close contact with minerals play key roles in the biogeochemical cycling of elements, soil formation, and plant nutrition. Yet, the composition of microbial communities inhabiting the mineralosphere (i.e., the soil surrounding minerals) is poorly understood. Here, we explored the composition of soil microbial communities associated with different types of minerals in various soil horizons. To this effect, a field experiment was set up in which mineral specimens of apatite, biotite, and oligoclase were buried in the organic, eluvial, and upper illuvial horizons of a podzol soil. After an incubation period of two years, the soil attached to the mineral surfaces was collected, and microbial communities were analyzed by means of Illumina MiSeq sequencing of the 16S (prokaryotic) and 18S (eukaryotic) ribosomal RNA genes. We found that both composition and diversity of bacterial, archaeal, and fungal communities varied across the different mineral surfaces, and that mineral type had a greater influence on structuring microbial assemblages than soil horizon. Thus, our findings emphasize the importance of mineral surfaces as ecological niches in soils.     

Spatial Patterns of Soil Microbial Communities in a Norway Spruce (Picea abies) Plantation

The phospholipid fatty acid (PLFA) profiles of soil microbial communities were determined in relation to the patterns of tree cover in a mature Norway spruce plantation. Replicate samples of the surface organic layers were taken close to the trunk, at 1 m and at 2 m (under the edge of the canopy) beneath five trees. Samples were analyzed for standard PLFAs to assess the initial composition of the microbial communities. Replicate samples were then incubated under constant or fluctuating moisture conditions for 30 d to test the hypothesis that the patterns of microbial community structure (or its physiological state) might be determined by biophysical conditions under the tree canopies. The PLFA profiles near the trunks and at 2 m were similar, but samples taken 1 m from the bases of the trees contained lower concentrations of polyunsaturated (fungal) and monounsaturated PLFAs, and higher concentrations of saturated PLFAs. These differences in PLFA profiles were maintained during laboratory incubation under a regime of drying and wetting cycles, but there was some evidence of convergence in community structure under constant moisture conditions resulting from significant increases and decreases in specific bacterial PLFA concentrations. There were no effects of either moisture treatment on fungal PLFA concentrations. It is concluded that variation in the soil biophysical environment beneath the tree canopies resulted in the differentiation of spatially defined bacterial communities that were tolerant of moisture stress. The anomaly that differences in community structure were largest at an intermediate position of 1 m between the trunk and below the canopy edge was not explained but may relate to tree root distribution.     

Soil Communities Promote Temporal Stability and Species Asynchrony in Experimental Grassland Communities

Background

Over the past two decades many studies have demonstrated that plant species diversity promotes primary productivity and stability in grassland ecosystems. Additionally, soil community characteristics have also been shown to influence the productivity and composition of plant communities, yet little is known about whether soil communities also play a role in stabilizing the productivity of an ecosystem.

Methodology/Principal Findings

Here we use microcosms to assess the effects of the presence of soil communities on plant community dynamics and stability over a one-year time span. Microcosms were filled with sterilized soil and inoculated with either unaltered field soil or field soil sterilized to eliminate the naturally occurring soil biota. Eliminating the naturally occurring soil biota not only resulted in lower plant productivity, and reduced plant species diversity, and evenness, but also destabilized the net aboveground productivity of the plant communities over time, which was largely driven by changes in abundance of the dominant grass Lolium perenne. In contrast, the grass and legumes contributed more to net aboveground productivity of the plant communities in microcosms where soil biota had been inoculated. Additionally, the forbs exhibited compensatory dynamics with grasses and legumes, thus lowering temporal variation in productivity in microcosms that received the unaltered soil inocula. Overall, asynchrony among plant species was higher in microcosms where an unaltered soil community had been inoculated, which lead to higher temporal stability in community productivity.

Conclusions/Significance

Our results suggest that soil communities increase plant species asynchrony and stabilize plant community productivity by equalizing the performance among competing plant species through potential antagonistic and facilitative effects on individual plant species.     

Impact of Fumigants on Soil Microbial Communities

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.     

Physiological Profiling of Soil Microbial Communities in a Florida Scrub-Oak Ecosystem: Spatial Distribution and Nutrient Limitations

Rapid physiological profiling of heterotrophic microbial communities enables intensive analysis of the factors affecting activity in aerobic habitats, such as soil. Previous methods for performing such profiling were severely limited due to enrichment bias and inflexibility in incubation conditions. We tested a new physiological profiling approach based on a microtiter plate oxygen sensor system (Becton Dickinson Oxygen Biosensor System (BDOBS)), which allows for testing of lower substrate addition (i.e., lower enrichment potential) and manipulation of physiochemical assay conditions, such as pH and nutrients. Soil microbial communities associated with a scrub-oak forest ecosystem on Merritt Island Wildlife Refuge in central Florida, USA, were studied in order to evaluate microbial activity in a nutrient poor soil and to provide baseline data on the site for subsequent evaluation of the effects of elevated CO₂ on ecosystem function. The spatial variation in physiological activity amongst different habitats (litter, bulk soil, and rhizosphere) was examined as a function of adaptation to local resources (i.e., water soluble extracts of roots and leaf litter) and the degree of N and P limitation. All the communities were primarily N-limited, with a secondary P limitation, which was greater in the rhizosphere and bulk soil. The litter community showed greater overall oxygen consumption when exposed to litter extracts relative to the rhizosphere or soil, suggesting acclimation toward greater use of the mixed substrates in the extract. Root extracts were readily used by communities from all the habitats with no habitat specific acclimation observed. A priming effect was detected in all habitats; addition of glucose caused a significant increase in the use of soil organic carbon. Response to added glucose was only observed with N and P addition, suggesting that C may be lost to the groundwater from these porous soils because nutrient limitation prevents C immobilization.     

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.     

Patterns in the Composition of Microbial Communities from a Subtropical River: Effects of Environmental,Spatial and Temporal Factors

Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO₄-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NO_x-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.     

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy.     

Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil

Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.     

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.     

Response of the Soil Microbial Community to Changes in Precipitation in a Semiarid Ecosystem

Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the structure and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation (+18%, −50%, or ambient) in a piñon-juniper woodland (Pinus edulis-Juniperus monosperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath piñon pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynamics, background climatic variability, and the composition of the associated aboveground community.