Fungal spore diversity of arbuscular mycorrhizal fungi associated with spring wheat: effects of tillage

We investigated the influence of tilling, N fertilization and crop stage on arbuscular mycorrhizae (AM) fungal species diversity in a wheat monoculture in the Pampa region of Argentina. Glomalean spores were isolated by wet sieving and decanting from conventionally tilled and nontilled soils cropped with wheat with or without N fertilization, at three phenological stages of the crop (tilling, flowering and grain filling) and fallow. Morphological characterization yielded at least 24 AM fungi taxa in the field samples, belonging to six genera of AMF: Acaulospora Archaeospora, Entrophospora, Gigaspora, Glomus and Scutellospora. Tilling and fertilization treatments did not result in decreased spore biodiversity. Wheat phenology influenced AM communities, with highest spore biodiversity during grain filling.     

Long‐term balanced fertilization increases the soil microbial functional diversity in a phosphorus‐limited paddy soil

The influence of long‐term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22‐year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array‐based analysis revealed that long‐term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer‐induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P‐limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.     

An evaluation of primers for detecting denitrifiers via their functional genes

Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio-environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrification rates are quite variable in time and space, and therefore difficult to model. Microbial ecology is working to improve the predictive ecology of denitrifiers by quantifying and describing the diversity of microbial functional groups. However, metagenomic sequencing has revealed previously undescribed diversity within these functional groups, and highlighted a need to reevaluate coverage of existing DNA primers for denitrification functional genes. We provide here a comprehensive in silico evaluation of primer sets that target diagnostic genes in the denitrification pathway. This analysis makes use of current DNA sequence data available for each functional gene. It contributes a comparative analysis of the strengths and limitations of each primer set for describing denitrifier functional groups. This analysis identifies genes for which development of new tools is needed, and aids in interpretation of existing datasets, both of which will facilitate application of molecular methods to further develop the predictive ecology of denitrifiers.     

Microbial activity and soil respiration under nitrogen addition in Alaskan boreal forest

Climate warming could increase rates of soil organic matter turnover and nutrient mineralization, particularly in northern high‐latitude ecosystems. However, the effects of increasing nutrient availability on microbial processes in these ecosystems are poorly understood. To determine how soil microbes respond to nutrient enrichment, we measured microbial biomass, extracellular enzyme activities, soil respiration, and the community composition of active fungi in nitrogen (N) fertilized soils of a boreal forest in central Alaska. We predicted that N addition would suppress fungal activity relative to bacteria, but stimulate carbon (C)‐degrading enzyme activities and soil respiration. Instead, we found no evidence for a suppression of fungal activity, although fungal sporocarp production declined significantly, and the relative abundance of two fungal taxa changed dramatically with N fertilization. Microbial biomass as measured by chloroform fumigation did not respond to fertilization, nor did the ratio of fungi : bacteria as measured by quantitative polymerase chain reaction. However, microbial biomass C : N ratios narrowed significantly from 16.0 ± 1.4 to 5.2 ± 0.3 with fertilization. N fertilization significantly increased the activity of a cellulose‐degrading enzyme and suppressed the activities of protein‐ and chitin‐degrading enzymes but had no effect on soil respiration rates or ¹⁴C signatures. These results indicate that N fertilization alters microbial community composition and allocation to extracellular enzyme production without affecting soil respiration. Thus, our results do not provide evidence for strong microbial feedbacks to the boreal C cycle under climate warming or N addition. However, organic N cycling may decline due to a reduction in the activity of enzymes that target nitrogenous compounds.     

Effects of long-term fertilization on AM fungal community structure and Glomalin-related soil protein in the Loess Plateau of China

Arbuscular mycorrhizal fungi (AMF) are crucial for ecosystem functioning, and thus have potential use for sustainable agriculture. In this study, we investigated the impact of organic and mineral fertilizers on the AMF community composition and content of Glomalin-related soil protein (GRSP) in a field experimental station which was established in 1979, in the Loess Plateau of China. Roots and soils were sampled three times during the growing period of winter wheat in 2008. The treatments including: N (inorganic N), NP (inorganic N and P), SNP (straw, inorganic N and P), M (farmyard manure), MNP (farmyard manure, inorganic N and P), and CK (no fertilization). AMF communities of root and soil samples were analyzed using PCR-DGGE, cloning and sequencing techniques; and GRSP content was determined by Bradford assay. Our results indicated that spore density, GRSP, and AMF community varied significantly in soils of long-term fertilization plots at three different wheat growing stages. The effects of wheat growing period on AMF community in roots were much more evident than fertilization regimes. However, the diversity of AMF was low in our study field. Up to five AMF phylotypes appeared in each sample, with the overwhelming dominance of a Glomus-like phylotype affiliated to G. mosseae. GRSP content was correlated positively with organic carbon, total phosphorus, available phosphorus, soil pH, and spore densities, but correlated negatively with soil C/N (P?<?0.05). The results of our study highlight that the richness of AMF in Loess Plateau agricultural region is low, and long-term fertilization, especially amendments with manure and straw, has beneficial effects on accumulation of soil organic carbon, spore density, GRSP content, and AMF diversity. Host phenology, edaphic factors (influenced by long-term fertilization), and habitats interacted to affect the AMF community and agoecosystem functioning. Additionally, soil moisture and pH make a greater contribution than other determined soil parameters to the AMF community dynamics in such a special semi-arid agroecosystem where crops rely greatly on rainfall.     

Soil Functional Operating Range Linked to Microbial Biodiversity and Community Composition Using Denitrifiers as Model Guild

Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.     

Chemistry and Microbial Functional Diversity Differences in Biofuel Crop and Grassland Soils in Multiple Geographies

We obtained soil samples from geographically diverse switchgrass (Panicum virgatum L.) and sorghum (Sorghum bicolor L.) crop sites and from nearby reference grasslands and compared their edaphic properties, microbial gene diversity and abundance, and active microbial biomass content. We hypothesized that soils under switchgrass, a perennial, would be more similar to reference grassland soils than sorghum, an annual crop. Sorghum crop soils had significantly higher NO₃ ^? -N, NH₄ ⁺ -N, SO₄ ^2? -S, and Cu levels than grassland soils. In contrast, few significant differences in soil chemistry were observed between switchgrass crop and grassland soils. Active bacterial biomass was significantly lower in sorghum soils than switchgrass soils. Using GeoChip 4.0 functional gene arrays, we observed that microbial gene diversity was significantly lower in sorghum soils than grassland soils. Gene diversity at sorghum locations was negatively correlated with NO₃ ^? -N, NH₄ ⁺ -N, and SO₄ ^2? -S in C and N cycling microbial gene categories. Microbial gene diversity at switchgrass sites varied among geographic locations, but crop and grassland sites tended to be similar. Microbial gene abundance did not differ between sorghum crop and grassland soils, but was generally lower in switchgrass crop soils compared to grassland soils. Our results suggest that switchgrass has fewer adverse impacts on microbial soil ecosystem services than cultivation of an annual biofuel crop such as sorghum. Multi-year, multi-disciplinary regional studies comparing these and additional annual and perennial biofuel crop and grassland soils are recommended to help define sustainable crop production and soil ecosystem service practices.     

A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling

The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high level of functional redundancy. As such, indices of species richness probably contribute little to understanding the functioning of soil ecosystems. Another approach stresses the value of identifying keystone organisms, that is those that play an exceptionally important role in determining the structure and function of ecosystems. Both views tend to ignore the importance of biodiversity in maintaining the numerous and complex interactions among organisms in soils and their contributions to biogeochemical cycling. We describe some of those interactions and their importance to ecosystem function.Soil organisms alter the physical, chemical and biological properties of soils in innumerable ways. The composition and structure of biotic communities at one hierarchical level can influence the spatial heterogeneity of resource and refuge patches at other hierarchical levels. This spatial heterogeneity is supported by a number of biologically relevant spheres of influence that include the detritusphere, the drilosphere, the porosphere, the aggregatusphere and the rhizosphere. Each has fairly distinct properties that operate at different spatial scales. We discuss how these properties may function in regulating the interactions among organisms and the biogeochemical processes that they mediate. It is through the formation of a spatially and temporally heterogeneous structure that biodiversity may contribute most significantly to the functioning of soil ecosystems. Real advances in understanding the significance of biodiversity to biogeochemical cycling will come from taking a broader view of biodiversity. Such a view will necessarily encompass many levels of resolution including: 1) the importance of biodiversity to specific biogenic transformations, 2) the complexity and specificity of biotic interactions in soils that regulate biogeochemical cycling, and 3) how biodiversity may operate at different hierarchically arranged spatial and temporal scales to influence the structure and function of ecosystems.     

The soil quality concept as a framework to assess management practices in vulnerable agroecosystems: A case study in Mediterranean vineyards

Land management aiming to sustain ecosystem services is an important issue, especially in biodiversity hot spots such as found in Mediterranean areas. In Mediterranean areas, viticulture is an important land use. Vineyards are frequently found on inherently poor soils and are submitted to intensive management practices, which threaten soil functioning and associated ecosystem services. To encourage winegrowers and stakeholders to be reflective and adapt their vineyard practices, we evaluated the effects of three soil management practices (inter row plant cover duration, weeding and fertilization strategies) on soil functioning in 146 commercial plots distributed in Southern France, by a complementary set of biological and physico-chemical indicators. We used the concept of soil dynamic quality to evaluate some soil management practices on soil functioning. The influence of inherent soil properties derived from pedogenesis on soil dynamic indicator response was accounted for by considering the response of soil indicators for three soil groups differing in their stoniness and Ca carbonate content. The three soil management practices systematically influenced some nematode-based indicators, whereas other indicators were ascribable to a specific soil type or practice. We demonstrated that the potential of soil management practices to enhance soil functioning is restricted by soil type. In particular for calcareous soils, the soil functioning is very stable limiting effects of soil management practices. The presence of a cover crop, even temporary, in the inter row, is the only practice which benefits soil functioning whatever the soil type whereas organic fertilization and chemical weeding exhibit contrasting results on soil functioning.     

Impacts of chronic nitrogen additions vary seasonally and by microbial functional group in tundra soils

Previous studies have shown that fertilization with nitrogen depresses overall microbial biomass and activity in soil. In the present study we broaden our understanding of this phenomenon by studying the seasonality of responses of specific microbial functional groups to chronic nitrogen additions in alpine tundra soils. We measured soil enzyme activities, mineralization kinetics for 8 substrates, biomass of 8 microbial functional groups, and changes in N and carbon pools in the soil. Our approach allowed us to compare the ability of the soil microbial biomass to utilize various substrates in addition to allowing us to estimate changes in biomass of microbial functional groups that are involved in carbon and nitrogen cycling. Overall microbial activity and biomass was reduced in fertilized plots, whereas pools of N in the soil and microbial biomass N were higher in fertilized plots. The negative effects of N were most prominent in the summer. Biomass of the dominant microbial functional groups recovered in fertilized soils during the winter and nitrogen storage in microbial biomass was higher in fertilized soils in the autumn and winter than in the summer. Microbial immobilization of N may therefore be a significant sink for added N during autumn and winter months when plants are not active. One large microbial group that did not recover in the winter in fertilized soils was phenol mineralizers, possibly indicating selection against microbes with enzyme systems for the breakdown of phenolic compounds and complex soil organic matter. Overall, this work is a step towards understanding how chronic N additions affect the structure and biogeochemical functioning of soil microbial communities.     

Biogeographic patterns in below-ground diversity in New York City's Central Park are similar to those observed globally

Soil biota play key roles in the functioning of terrestrial ecosystems, however, compared to our knowledge of above-ground plant and animal diversity, the biodiversity found in soils remains largely uncharacterized. Here, we present an assessment of soil biodiversity and biogeographic patterns across Central Park in New York City that spanned all three domains of life, demonstrating that even an urban, managed system harbours large amounts of undescribed soil biodiversity. Despite high variability across the Park, below-ground diversity patterns were predictable based on soil characteristics, with prokaryotic and eukaryotic communities exhibiting overlapping biogeographic patterns. Further, Central Park soils harboured nearly as many distinct soil microbial phylotypes and types of soil communities as we found in biomes across the globe (including arctic, tropical and desert soils). This integrated cross-domain investigation highlights that the amount and patterning of novel and uncharacterized diversity at a single urban location matches that observed across natural ecosystems spanning multiple biomes and continents.     

Rapid change of AM fungal community in a rain-fed wheat field with short-term plastic film mulching practice

Plastic film mulching (PFM) is a widely used agricultural practice in the temperate semi-arid Loess Plateau of China. However, how beneficial soil microbes, arbuscular mycorrhizal (AM) fungi in particular, respond to the PFM practice is not known. Here, a field experiment was performed to study the effects of a 3-month short-term PFM practice on AM fungi in plots planted with spring wheat (Triticum aestivum L. cv. Dingxi-2) in the Loess Plateau. AM colonization, spore density, wheat spike weight, and grain phosphorus (P) content were significantly increased in the PFM treatments, and these changes were mainly attributable to changes in soil properties such as available P and soil moisture. Alkaline phosphatase activity was significantly higher in PFM soils, but levels of AM fungal-related glomalin were similar between treatments. A total of nine AM fungal phylotypes were detected in root samples based on AM fungal SSU rDNA analyses, with six and five phylotypes in PFM and no-PFM plots, respectively. Although AM fungal phylotype richness was not statistically different between treatments, the community compositions were different, with four and three specific phylotypes in the PFM and no-PFM plots, respectively. A significant and rapid change in AM fungal, wheat, and soil variables following PFM suggested that the functioning of the AM symbiosis had been changed in the wheat field under PFM. Future studies are needed to investigate whether PFM applied over a longer term has a similar effect on the AM fungal community and their functioning in an agricultural ecosystem.     

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant–mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil–plant continuums (rhizosphere, phyllosphere and endosphere) in the maize–wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.     

Soil minerals affect taxon-specific bacterial growth

Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages—particularly short-range order minerals—affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with ¹⁸O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25–36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.Subject terms: Biogeochemistry, Microbial ecology, Biogeochemistry     

A genomic view of the microbiome of coral reef demosponges

Sponges underpin the productivity of coral reefs, yet few of their microbial symbionts have been functionally characterised. Here we present an analysis of ~1200 metagenome-assembled genomes (MAGs) spanning seven sponge species and 25 microbial phyla. Compared to MAGs derived from reef seawater, sponge-associated MAGs were enriched in glycosyl hydrolases targeting components of sponge tissue, coral mucus and macroalgae, revealing a critical role for sponge symbionts in cycling reef organic matter. Further, visualisation of the distribution of these genes amongst symbiont taxa uncovered functional guilds for reef organic matter degradation. Genes for the utilisation of sialic acids and glycosaminoglycans present in sponge tissue were found in specific microbial lineages that also encoded genes for attachment to sponge-derived fibronectins and cadherins, suggesting these lineages can utilise specific structural elements of sponge tissue. Further, genes encoding CRISPR and restriction-modification systems used in defence against mobile genetic elements were enriched in sponge symbionts, along with eukaryote-like gene motifs thought to be involved in maintaining host association. Finally, we provide evidence that many of these sponge-enriched genes are laterally transferred between microbial taxa, suggesting they confer a selective advantage within the sponge niche and therefore play a critical role in host ecology and evolution.Subject terms: Microbial ecology, Metagenomics, Symbiosis     

The response of heterotrophic activity and carbon cycling to nitrogen additions and warming in two tropical soils

Nitrogen (N) deposition is projected to increase significantly in tropical regions in the coming decades, where changes in climate are also expected. Additional N and warming each have the potential to alter soil carbon (C) storage via changes in microbial activity and decomposition, but little is known about the combined effects of these global change factors in tropical ecosystems. In this study, we used controlled laboratory incubations of soils from a long‐term N fertilization experiment to explore the sensitivity of soil C to increased N in two N‐rich tropical forests. We found that fertilization corresponded to significant increases in bulk soil C concentrations, and decreases in C loss via heterotrophic respiration (P< 0.05). The increase in soil C was not uniform among C pools, however. The active soil C pool decomposed faster with fertilization, while slowly cycling C pools had longer turnover times. These changes in soil C cycling with N additions corresponded to the responses of two groups of microbial extracellular enzymes. Smaller active C pools corresponded to increased hydrolytic enzyme activities; longer turnover times of the slowly cycling C pool corresponded to reduced activity of oxidative enzymes, which degrade more complex C compounds, in fertilized soils. Warming increased soil respiration overall, and N fertilization significantly increased the temperature sensitivity of slowly cycling C pools in both forests. In the lower elevation forest, respired CO₂ from fertilized cores had significantly higher Δ¹⁴C values than control soils, indicating losses of relatively older soil C. These results indicate that soil C storage is sensitive to both N deposition and warming in N‐rich tropical soils, with interacting effects of these two global change factors. N deposition has the potential to increase total soil C stocks in tropical forests, but the long‐term stability of this added C will likely depend on future changes in temperature.     

Nitrogen mineralization and potential nitrification at different depths in acid forest soils

Yield decline of cereals grown in monoculture may be alleviated with alternative crop management strategies. Crop rotation and optimized tillage and fertilizer management can contribute to more sustainable food and fiber production in the long-term by increasing diversity, maintaining soil organic matter (SOM), and reducing adverse effects of excessive N application on water quality. We investigated the effects of crop sequence, tillage, and N fertilization on long-term grain production on an alluvial, silty clay loam soil in southcentral Texas. Crop sequences consisted of monoculture sorghum (Sorghum bicolor (L.) Moench,) wheat (Triticum aestivum L.), and soybean (Glycine max (L.) Merr), wheat/soybean double-crop, and rotation of sorghum with wheat/soybean. Grain yields tended to be lower with no tillage (NT) than with conventional tillage (CT) early in the study and became more similar after 11 years. Nitrogen fertilizer required to produce 95% to maximum sorghum yield was similar for monoculture and rotation upon initiation of the experiment and averaged 16 and 11 mg N g^-1 grain with NT and CT, respectively. After 11 years, however, the N fertilizer requirement became similar for both tillage regimes, but was greater in monoculture (17 mg N g^-1 grain) than in rotation (12 mg N g^-1 grain). Crop sequences with double-cropping resulted in greater land use efficiency because similar or lower amounts of N fertilizer were required to produce equivalent grain than with less intensive monoculture systems. These more intensive crop sequences produced more stover with higher N quality primarily due to the inclusion of soybean in the rotation. Large quantities of stover that remained on the soil surface with NT led to greater SOM content, which increased the internal cycling of nutrients in this soil. In southcentral Texas, where rainfall averages nearly 1000 mm yr^-1, more intensive cropping of sorghum, wheat, and soybean with moderate N fertilization using reduced tillage can increase grain production and potentially decrease N losses to the environment by cycling more N into the crop-SOM system.     

Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community

As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.     

Soil Fertility and the Impact of Exotic Invasion on Microbial Communities in Hawaiian Forests

Exotic plant invasions into Hawaiian montane forests have altered many important nutrient cycling processes and pools. Across different ecosystems, researchers are uncovering the mechanisms involved in how invasive plants impact the soil microbial community-the primary mediator of soil nutrient cycling. We examined whether the invasive plant, Hedychium gardnerianum, altered microbial community composition in forests dominated by a native tree, Metrosideros polymorpha, under varying soil nutrient limitations and soil fertility properties within forest plots of the Hawaii long-term substrate age gradient (LSAG). Microbial community lipid analysis revealed that when nutrient limitation (as determined by aboveground net primary production [ANPP]) and soil fertility were taken into account, plant species differentially altered soil microbial community composition. Microbial community characteristics differed under invasive and native plants primarily when N or P was added to the older, highly weathered, P-limited soils. Long-term fertilization with N or P at the P-limited site led to a significant increase in the relative abundance of the saprophytic fungal indicator (18:2 omega 6c,9c) under the invasive plant. In the younger, N-limited soils, plant species played a minor role in influencing soil microbial community composition. We found that the general rhizosphere microbial community structure was determined more by soil fertility than by plant species. This study indicates that although the aggressive invasion of a nutrient-demanding, rapidly decomposable, and invasive plant into Hawaiian forests had large impacts on soil microbial decomposers, relatively little impact occurred on the overall soil microbial community structure. Instead, soil nutrient conditions were more important determinants of the overall microbial community structure within Hawaii's montane forests.     

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.