Impact of different bioenergy crops on N-cycling bacterial and archaeal communities in soil

Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines

Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.

Characterization of the responses of soil micro-organisms to azoxystrobin and the residue dynamics of azoxystrobin in wheat-corn rotation fields over two years

Azoxystrobin, a high-efficiency and broad-spectrum strobilurin fungicide, has been widely used in global agricultural production. However, the effects of azoxystrobin on soil micro-organisms have scarcely been studied, and relevant experiments are usually conducted under laboratory conditions using active ingredient. Therefore, the effects of azoxystrobin on soil micro-organisms when applied to actual farmland are unknown. We sought to address this knowledge gap in this study, where we studied the effects of azoxystrobin on soil micro-organisms in a wheat-corn rotation field over two years. The results indicate that after two years of azoxystrobin application the activities of soil enzymes were inhibited, and the abundance of functional genes related to the nitrogen and carbon cycle were inhibited, which change the abundance of soil microbial bacteria of genera. As a consequence, the soil nitrogen and carbon cycles were disturbed. In addition, azoxystrobin inhibited the abundance of functional bacteria related to organic pollutant degradation and soil metabolism, where the rate of azoxystrobin degradation diminished over time. Moreover, azoxystrobin significantly inhibited the soil-culturable microbial population. The integrated biomarker response (IBR) indicated that the soil-culturable microbial population can be used as a sensitive indicator of the effect of azoxystrobin on soil micro-organisms. The final levels of azoxystrobin residues measured in grains were less than 0.004 mg/kg, lower than the maximum residue limits in European Union and China. The results of this study provide a basis for suggestions regarding the appropriate use of azoxystrobin in addition to support for elucidating the interaction between biological macromolecules and pollutants.

Urea fertilization and grass species alter microbial nitrogen cycling capacity and activity in a C4 native grassland

Soil microbial transformation of nitrogen (N) in nutrient-limited native C₄ grasslands can be affected by N fertilization rate and C₄ grass species. Here, we report in situ dynamics of the population size (gene copy abundances) and activity (transcript copy abundances) of five functional genes involved in soil N cycling (nifH, bacterial amoA, nirK, nirS, and nosZ) in a field experiment with two C₄ grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) under three N fertilization rates (0, 67, and 202 kg N ha^-1). Diazotroph (nifH) abundance and activity were not affected by N fertilization rate nor grass species. However, moderate and high N fertilization promoted population size and activity of ammonia oxidizing bacteria (AOB, quantified via amoA genes and transcripts) and nitrification potential. Moderate N fertilization increased abundances of nitrite-reducing bacterial genes (nirK and nirS) under switchgrass but decreased these genes under big bluestem. The activity of nitrous oxide reducing bacteria (nosZ transcripts) was also promoted by moderate N fertilization. In general, high N fertilization had a negative effect on N-cycling populations compared to moderate N addition. Compared to big bluestem, the soils planted with switchgrass had a greater population size of AOB and nitrite reducers. The significant interaction effects of sampling season, grass species, and N fertilization rate on N-cycling microbial community at genetic-level rather than transcriptional-level suggested the activity of N-cycling microbial communities may be driven by more complex environmental factors in native C₄ grass systems, such as climatic and edaphic factors.

Achieving simultaneous nitrification, denitrification, and phosphorus removal in pilot-scale flow-through biofilm reactor with low dissolved oxygen concentrations: Performance and mechanisms

In this pilot-scale study, a flow-through biofilm reactor (FTBR) was investigated for municipal wastewater treatment. The removal efficiencies for ammonium, total nitrogen, total phosphorus, and chemical oxygen demand were 87.2 ± 17.9%, 61.1 ± 13.9%, 83.5 ± 11.9%, and 92.6 ± 1.7%, respectively, at low dissolved oxygen concentrations (averaged at 0.59 mg/L), indicating the feasibility and robustness of the FTBR for a simultaneous nitrification, denitrification, and phosphorous removal (SNDPR) process. The co-occurrence network of bacteria in the dynamic biofilm was complex, with equivalent bacterial cooperation and competition. Nevertheless, the bacterial interactions in the suspended sludge were mainly cooperative. The presence of dynamic biofilms increased bacterial diversity by creating niche differentiation, which enriched keystone species closely related to nutrient removal. Overall, this study provides a novel FTBR-based SNDPR process and reveals the ecological mechanisms responsible for nutrient removal.

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production. IMPORTANCEMiscanthus × giganteus is a promising candidate for bioeconomy cropping systems; however, it remains unclear how the soil microbiome supplies nitrogen to this low-input crop. DNA-based techniques are used to provide community characterization, but may miss important metabolically active taxa. By analyzing both DNA- and actively transcribed RNA-based microbial communities, we found that nitrogen cycling taxa in the soil microbiome may be underestimated using only DNA-based approaches. Accurately understanding the role of microbes and how they cycle nutrients is important for the development of sustainable bioenergy crops, and RNA-based approaches are recommended as a complement to DNA approaches to better understand the microbial, plant, and management interactions.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

Site and Bioenergy Cropping System Similarly Affect Distinct Live and Total Soil Microbial Communities

Bioenergy crops are a promising energy alternative to fossil fuels. During bioenergy feedstock production, crop inputs shape the composition of soil microbial communities, which in turn influences nutrient cycling and plant productivity. In addition to cropping inputs, site characteristics (e.g., soil texture, climate) influence bacterial and fungal communities. We explored the response of soil microorganisms to bioenergy cropping system (switchgrass vs. maize) and site (sandy loam vs. silty loam) within two long-term experimental research stations. The live and total microbial community membership was investigated using 16S and ITS amplicon sequencing of soil RNA and DNA. For both nucleic acid types, we expected fungi and prokaryotes to be differentially impacted by crop and site due their dissimilar life strategies. We also expected live communities to be more strongly affected by site and crop than the total communities due to a sensitivity to recent stimuli. Instead, we found that prokaryotic and fungal community composition was primarily driven by site with a secondary crop effect, highlighting the importance of soil texture and fertility in shaping both communities. Specific highly abundant prokaryotic and fungal taxa within live communities were indicative of site and cropping systems, providing insight into treatment-specific, agriculturally relevant microbial taxa that were obscured within total community profiles. Within live prokaryote communities, predatory Myxobacteria spp. were largely indicative of silty and switchgrass communities. Within live fungal communities, Glomeromycota spp. were solely indicative of switchgrass soils, while a few very abundant Mortierellomycota spp. were indicative of silty soils. Site and cropping system had distinct effects on the live and total communities reflecting selection forces of plant inputs and environmental conditions over time. Comparisons between RNA and DNA communities uncovered live members obscured within the total community as well as members of the relic DNA pool. The associations between live communities and relic DNA are a product of the intimate relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter, and in turn shapes soil microbial dynamics.

Nitrogen Fertilization and Native C4 Grass Species Alter Abundance, Activity, and Diversity of Soil Diazotrophic Communities

Native C4 grasses have become the preferred species for native perennial pastures and bioenergy production due to their high productivity under low soil nitrogen (N) status. One reason for their low N requirement is that C4 grasses may benefit from soil diazotrophs and promote biological N fixation. Our objective was to evaluate the impact of N fertilization rates (0, 67, and 202 kg N ha-1) and grass species (switchgrass [Panicum virgatum] and big bluestem [Andropogon gerardii]) on the abundance, activity, diversity, and community composition of soil diazotrophs over three agricultural seasons (grass green-up, initial harvest, and second harvest) in a field experiment in East Tennessee, United States. Nitrogen fertilization rate had a stronger influence on diazotroph population size and activity (determined by nifH gene and transcript abundances) and community composition (determined by nifH gene amplicon sequencing) than agricultural season or grass species. Excessive fertilization (202 kg N ha-1) resulted in fewer nifH transcripts compared to moderate fertilization (67 kg N ha-1) and decreased both richness and evenness of diazotrophic community, reflecting an inhibitory effect of high N application rates on soil diazotrophic community. Overall, cluster I and cluster III diazotrophs were dominant in this native C4 grass system. Diazotroph population size and activity were directly related to soil water content (SWC) based on structural equation modeling. Soil pH, SWC, and C and N availability were related to the variability of diazotrophic community composition. Our results revealed relationships between soil diazotrophic community and associated soil properties, adding to our understanding of the response of soil diazotrophs to N fertilization and grass species in native C4 grass systems.

Conversion of marginal land into switchgrass conditionally accrues soil carbon but reduces methane consumption

Switchgrass is a deep-rooted perennial native to the US prairies and an attractive feedstock for bioenergy production; when cultivated on marginal soils it can provide a potential mechanism to sequester and accumulate soil carbon (C). However, the impacts of switchgrass establishment on soil biotic/abiotic properties are poorly understood. Additionally, few studies have reported the effects of switchgrass cultivation on marginal lands that have low soil nutrient quality (N/P) or in areas that have experienced high rates of soil erosion. Here, we report a comparative analyses of soil greenhouse gases (GHG), soil chemistry, and microbial communities in two contrasting soil types (with or without switchgrass) over 17 months (1428 soil samples). These soils are highly eroded, ‘Dust Bowl’ remnant field sites in southern Oklahoma, USA. Our results revealed that soil C significantly increased at the sandy-loam (SL) site, but not at the clay-loam (CL) site. Significantly higher CO₂ flux was observed from the CL switchgrass site, along with reduced microbial diversity (both alpha and beta). Strikingly, methane (CH₄) consumption was significantly reduced by an estimated 39 and 47% at the SL and CL switchgrass sites, respectively. Together, our results suggest that soil C stocks and GHG fluxes are distinctly different at highly degraded sites when switchgrass has been cultivated, implying that carbon balance considerations should be accounted for to fully evaluate the sustainability of deep-rooted perennial grass cultivation in marginal lands.

Influence of shrub willow buffers strategically integrated in an Illinois corn-soybean field on soil health and microbial community composition

Soil serves many important ecological functions and is an integral part of our existence as a society. However, concerns for soil health are growing globally, in part due to the negative impacts of agricultural management on soil resources. The production of perennial bioenergy crops on marginal land in row-crop production systems is one solution that could improve land-use efficiency and address the sustainability of cropland management. Because the relationship between crop management and the environment is complex, more research is needed to evaluate the potential benefits perennial bioenergy crop production has on soil health, as well as other ecosystem services. In this study, shrub willow buffers were strategically integrated into a corn-soybean cropping system with the main objective of reducing nitrate-N leaching from grain crop production while producing biomass for bioenergy. Two buffer systems (defined by landscape positions) were included for comparison, one on marginal land with exposure to nitrate-N leaching from upslope grain (southern plots) and one on fertile soils with less nitrate-N leaching potential (northern plots). Evaluation of soil (chemistry, bulk density, microbial community) and shrub willow vegetation properties (fine roots, leaf litter decomposition, and nutrient uptake dynamics), showed that landscape position plays an important role in (1) the dynamics of soil chemical properties, (2) shrub willow's influence and productivity, and (3) the provision of additional ecosystem services such as reductions in nitrous oxide emissions and nitrate-N leaching. In addition, the combination of crop type and landscape position (N-grain, N-willow, S-grain, and S-willow) influenced the species composition of the soil microbial community, resulting in unique and identifiable communities. These results highlight the potential application of shrub willow buffers for ecosystem service provision and support of ecosystem processes; however, understanding the relationship between the microbial community, crop type, and landscape is important for understanding the sustainability of the design.

Elevational is the main factor controlling the soil microbial community structure in alpine tundra of the Changbai Mountain

To reveal the self-coordination mechanism of the fragile ecosystem of alpine tundra, we explored the relationship between soil microorganisms and other elements. On the alpine tundra of the Changbai Mountain, different vegetation types, altitudes and soil properties were selected as driving factors of soil microbial community. Soil microbial community, C- and N-cycling functional microbial and fungal biomass were analyzed. Structural equation model was used to study the control of biotic and abiotic factors in rhizosphere soil microbial community. The results showed that the pH value of soil had the strongest direct impact on the diversity and community structure of soil microorganisms, and had significant correlation with most of the C- and N-cycling functional microbial; organic carbon and vegetation also have strongest direct effect on fungal biomass, but all of them were not main factors influence soil microbial community structure, the elevation was the main controlling factor. In addition, the elevation mainly through indirect action affects the soil microbial community by driving distribution of plant species, soil organic carbon and pH value. This finding highlighted that elevation was the main predictor to determine rhizosphere microbial community structure but not vegetation in alpine tundra of Changbai Mountain.

Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses

Soil microbes play important roles in plant growth and in the biogeochemical cycling of earth's elements. However, the structure and functions of the microbial community associated with the growth of second-generation energy crops, such as Miscanthus, remain unclear. Thus, in this study, the composition and function of the bacterial and fungal communities associated with Miscanthus cultivation were analyzed by MiSeq sequencing combined with PICRUSt and FUNGUIld analyses. The results of community composition and diversity index analyses showed that Miscanthus cultivation significantly altered the bacterial and fungal community composition and reduced bacterial and fungal diversity. In addition, Miscanthus cultivation increased the soil organic matter (SOM) and total nitrogen (TN) contents. The correlation analysis between microbial community composition and environmental factors indicated that SOM and TN were the most important factors affecting bacterial and fungal communities. Miscanthus cultivation could enrich the abundances of Pseudomonas, Rhizobium, Luteibacter, Bradyrhizobium, Phenylobacterium and other common plant-promoting bacteria, while also increasing Cladophialophora, Hymenula, Magnaporthe, Mariannaea, etc., which predicted corresponded to the saprotrophic, plant pathogenic, and pathotrophic trophic modes. The PICRUSt predictive analysis indicated that Miscanthus cultivation altered the metabolic capabilities of bacterial communities, including the metabolism of carbon, nitrogen, and phosphorus cycle. In addition, FUNGUIld analysis indicated that Miscanthus cultivation altered the fungal trophic mode. The effects of Miscanthus on the communities and function of bacteria and fungi varied among Miscanthus species. Miscanthus specie Xiangdi NO 1 had the greatest impact on soil bacterial and fungal communities, whereas Miscanthus specie Wujiemang NO 1 had the greatest impact on soil bacteria and fungi functions. The results of this study provide a reference for the composition and function of microbial communities during the growth of Miscanthus.

Nitrogen fertilizer is a key factor affecting the soil chemical and microbial communities in a Mollisol

Microbial communities drive geochemical cycles in soils. Relatively few studies have assessed the long-term impacts of different types of soil amendments under field conditions in long-term experiments. The response of soil microbial organisms in a Mollisol cultivated with maize for 35 years was examined. Treatments involved the use of N, P, and K fertilizers and two doses of straw residue in isolation or combined. Real-time PCR and Illumina MiSeq sequencing methods were used to characterize the microbial community. The results showed that addition of nitrogen fertilizers decreased soil pH, but this was mitigated when a high dose of straw was also incorporated. Long-term application of inorganic fertilizers was able to alter the abundance of functional soil microbial population. Application of inorganic N fertilizer resulted in distinctive changes on N-cycle microorganisms. Phosphate-solubilizing functional genes abundance was lower in plots with no phosphate fertilizer. Sequencing analysis showed that the presence or absence of N in the fertilizer mix is a key factor affecting bacterial community diversity of agricultural soil, and pH, total organic C, and total N show a high correlation with bacterial community composition. Nitrogen addition increased the N concentration in the soil, which could cause changes in the soil pH and change the soil bacterial community. Our findings proved that interaction of N fertilizer with other fertilizers can affect microbial communities.

Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil

Bioremediation of organic pollutants has been identified as an economically efficient and environmentally friendly method. Here, a pot experiment was conducted to evaluate the bioremediation efficiency of dibutyl phthalate (DBP) by Gordonia phthalatica sp. nov. QH-11 in agricultural soils, along with the effect of this exogenous organism on the native microbial community and ecosystem functions during the bioremediation process. The results showed that inoculation with strain QH-11 accelerated DBP degradation in the soil and decreased DBP accumulation in plants, thereby reducing the health risks associated with vegetables grown in those soils. High-throughput sequencing demonstrated that both DBP contamination and the bioremediation process significantly altered prokaryotic community composition, structure, and network interactions; however, these effects were greatly reduced after 30 d. Dibutyl phthalate affected the prokaryotic community by influencing soil properties rather than directly impacting on microorganisms. In addition, ecosystem functions, like the nitrogen cycle, were significantly altered. Contamination with DBP promoted nitrogen fixation and the denitrification processes while inhibiting nitrification. Bioremediation may mitigate some of the changes to nitrogen cycling, helping to maintain the balance of prokaryotic community function. According to this study, bioremediation through highly efficient degradation bacteria may be a safe and promising method for reducing PAEs contamination in soil-vegetable systems.

Achieving mainstream nitrogen removal through simultaneous partial nitrification, anammox and denitrification process in an integrated fixed film activated sludge reactor

The anaerobic ammonium oxidation (anammox) is becoming a critical technology for energy neutral in mainstream wastewater treatment. However, the presence of chemical oxygen demanding in influent would result in a poor nitrogen removal efficiency during the deammonification process. In this study, the simultaneous partial nitrification, anammox and denitrification process (SNAD) for mainstream nitrogen removal was investigated in an integrated fixed film activated sludge (IFAS) reactor. SNAD-IFAS process achieved a total nitrogen (TN) removal efficiency of 72 ± 2% and an average COD removal efficiency was 88%. The optimum COD/N ratio for mainstream wastewater treatment was 1.2 ± 0.2. Illumina sequencing analysis and activity tests showed that anammox and denitrifying bacteria were the dominant nitrogen removal microorganism in the biofilm and the high COD/N ratios (≥2.0) leaded to the proliferation of heterotrophic bacteria (Hydrogenophaga) and nitrite-oxidizing bacteria (Nitrospira) in the suspended sludge. Network analysis confirmed that anammox bacteria (Candidatus Kuenenia) could survive in organic matter environment due to that anammox bacteria displayed significant co-occurrence through positive correlations with some heterotrophic bacteria (Limnobacter) which could protect anammox bacteria from hostile environments. Overall, the results of this study provided more comprehensive information regarding the community composition and assemblies in SNAD-IFAS process for mainstream nitrogen removal.

Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence

Disentangling the relative influences of soil properties and plant-host on root-associated microbiomes in natural systems is challenging, given that spatially segregated soil types display distinct historical legacies. In addition, distant locations may also lead to biogeographical patterns of microbial communities. Here, we used an undisturbed salt marsh chronosequence spanning over a century of ecosystem development to investigate changes in the community composition and abundance of a set of nitrogen-cycling genes. Specifically, we targeted genes of diazotrophs and ammonia oxidizers associated with the bulk and rhizosphere soil of the plant species Limonium vulgare. Samples were collected across five distinct successional stages of the chronosequence (ranging from 5 to 105 years) at two time-points. Our results indicate that soil variables such as sand:silt:clay % content and pH strongly relates to the abundance of N-cycling genes in the bulk soil. However, in the rhizosphere samples, the abundance of ammonia-oxidizing organisms (both bacteria and archaea, AOB and AOA, respectively) was relatively constant across most of the successional stages, albeit displaying seasonal variation. This result indicates a potentially stronger control of plant host (rather than soil) on the abundance of these organisms. Interestingly, the plant host did not have a significant effect on the composition of AOA and AOB communities, being mostly divergent according to soil successional stages. The abundance of diazotrophic communities in rhizosphere samples was more affected by seasonality than those of bulk soil. Moreover, the abundance pattern of diazotrophs in the rhizosphere related to the systematic increase of plant biomass and soil organic matter along the successional gradient. These results suggest a potential season-dependent regulation of diazotrophs exerted by the plant host. Overall, this study contributes to a better understanding of how the natural formation of a soil and host plants influence the compositional and abundance changes of nitrogen-cycling genes in bulk and rhizosphere soil microhabitats.

COREMIC: a web-tool to search for a niche associated CORE MICrobiome

Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram of soil. Understanding how this diversity is sorted and selected into habitat niches is a major focus of ecology and biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases to show how it can be used to answer questions related to the core microbiome of habitat-microbe relationships. By making use of the burgeoning growth of information from databases, our tool “COREMIC” meets a great need in the search for understanding niche partitioning and habitat-function relationships. The work is unique, furthermore, because it provides a user-friendly statistically robust web-tool (http://coremic2.appspot.com or http://core-mic.com), developed using Google App Engine, to help in the process of database mining to identify the “core microbiome” associated with a given habitat. A case study is presented using data from 31 switchgrass rhizosphere community habitats across a diverse set of soil and sampling environments. The methodology utilizes an outgroup of 28 non-switchgrass (other grasses and forbs) to identify a core switchgrass microbiome. Even across a diverse set of soils (five environments), and conservative statistical criteria (presence in more than 90% samples and FDR q-val <0.05% for Fisher’s exact test) a core set of bacteria associated with switchgrass was observed. These included, among others, closely related taxa from Lysobacter spp., Mesorhizobium spp, and Chitinophagaceae. These bacteria have been shown to have functions related to the production of bacterial and fungal antibiotics and plant growth promotion. COREMIC can be used as a hypothesis generating or confirmatory tool that shows great potential for identifying taxa that may be important to the functioning of a habitat (e.g. host plant). The case study, in conclusion, shows that COREMIC can identify key habitat-specific microbes across diverse samples, using currently available databases and a unique freely available software.

Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China

Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.

Cellulosic biofuel contributions to a sustainable energy future: Choices and outcomes

Cellulosic crops are projected to provide a large fraction of transportation energy needs by mid-century. However, the anticipated land requirements are substantial, which creates a potential for environmental harm if trade-offs are not sufficiently well understood to create appropriately prescriptive policy. Recent empirical findings show that cellulosic bioenergy concerns related to climate mitigation, biodiversity, reactive nitrogen loss, and crop water use can be addressed with appropriate crop, placement, and management choices. In particular, growing native perennial species on marginal lands not currently farmed provides substantial potential for climate mitigation and other benefits.

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot-1, respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg-1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems.

Rhododendron aureum Georgi formed a special soil microbial community and competed with above-ground plants on the tundra of the Changbai Mountain, China

Rhododendron aureum Georgi is a perennial evergreen dwarf shrub that grows at all elevations within the alpine tundra of northern China. Previous research has investigated the plant communities of R. aureum; however, little information is available regarding interspecific competition and underground soil microbial community composition. The objective of our study was to determine whether the presence of R. aureum creates a unique soil microbiome and to investigate the relationship between R. aureum and other plant species. Our study site ranged from 1,800 to 2,600 m above sea level on the northern slope of the Changbai Mountain. The results show that the soil from sites with an R. aureum community had a higher abundance of nitrogen-fixing bacteria and a higher resistance to pathogens than soils from sites without R. aureum. We emphasize that R. aureum promotes a unique soil microbial community structure that is distinct from those associated with other plants. Elevation and microbial biomass were the main influencing factors for plant community structure. Analysis of interspecific relationships reveals that R. aureum is negatively associated with most other dominant shrubs and herbs, suggesting interspecific competition. It is necessary to focus on other dominant species if protection and restoration of the R. aureum competition is to occur. In the future, more is needed to prove whether R. aureum decreases species diversity in the tundra ecosystems of Changbai Mountain.

The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands

The establishment of energy crops could be an option for the management of degraded and contaminated lands, where they would not compete with food production for land use. Here, we aimed to explore the potential of certain native Mediterranean species for the revegetation of contaminated lands for energy production purposes. A field survey was conducted in a trace-element (TE) contaminated area from SW Spain, where the patterns of biomass production, TE accumulation and the calorific value of some thistle species were analyzed along a soil contamination gradient. In a greenhouse experiment the response of two thistle species (Cynara cardunculus and Silybum marianum) and the shrub Dittrichia viscosa to soil contamination was assessed, as well as the effects of these species on some soil microbial parameters involved in nutrient cycling (enzyme activities and arbuscular mycorrhizal colonization in roots). Silybum marianum was able to colonize highly contaminated soils. Its aboveground biomass accumulated Cd and had a relatively high calorific value; this value was similar in biomass obtained from both heavily and moderately contaminated soils. Greenhouse experiment confirmed that S. marianum biomass production and calorific value is scarcely affected by soil contamination. In addition, some soil enzyme activities were clearly enhanced in the S. marianum rhizosphere. Dittrichia viscosa is another promising species, given its capacity to produce a high biomass with appreciable calorific value in acid contaminated soils. Germination of both species was hampered in the acid contaminated soil, and therefore soil pH correction would have to be accomplished before establishing these species on extremely acid soils. Further assessment of the risk of transfer of Cd and other TE to the food chain would be needed to confirm the suitability of these species for the revegetation of contaminated lands with energy production purposes.

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation

Switchgrass (Panicum virgatum L.) is a cellulosic biofuel feedstock and their effects on bacterial communities in deep soils remain poorly understood. To reveal the responses of bacterial communities to long-term switchgrass cultivation through the soil profile, we examined the shift of soil microbial communities with depth profiles of 0–60 cm in five-year switchgrass cultivation and fallow plots. The Illumina sequencing of the 16S rRNA gene showed that switchgrass cultivation significantly increased microbial OTU richness, rather than microbial Shannon diversity; however, there was no significant difference in the structure of microbial communities between switchgrass cultivation and fallow soils. Both switchgrass cultivation and fallow soils exhibited significant negative vertical spatial decay of microbial similarity, indicating that more vertical depth distant soils had more dissimilar communities. Specifically, switchgrass cultivation soils showed more beta-diversity variations across soil depth profile. Through network analysis, more connections and closer relationships of microbial taxa were observed in soils under switchgrass cultivation, suggesting that microbial co-occurrence patterns were substantially influenced by switchgrass cultivation. Overall, our study suggested that five-year switchgrass cultivation could generated more beta-diversity variations across soil depth and more complex inter-relationships of microbial taxa, although did not significantly shape the structure of soil microbial community.

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra

Deyeuxia angustifolia (Komarov) Y. L Chang is an herb species originating from the birch forests in the Changbai Mountain. Recently, this species has been found encroaching into large areas in the western slopes of the alpine tundra in the Changbai Mountain, threatening the tundra ecosystem. In this study, we systematically assessed the response of the rhizosphere soil microbial to D. angustifolia encroaching in alpine tundra by conducting experiments for two vegetation types (shrubs and herbs) by real-time PCR and Illumina Miseq sequencing methods. The treatments consisted of D. angustifolia sites (DA), native sites (NS, NH) and encroaching sites (ES, EH). Our results show that (1) Rhizosphere soil properties of the alpine tundra were significantly impacted by D. angustifolia encroaching; microbial nutrient cycling and soil bacterial communities were shaped to be suitable for D. angustifolia growth; (2) The two vegetation community rhizosphere soils responded differently to D. angustifolia encroaching; (3) By encroaching into both vegetation communities, D. angustifolia could effectively replace the native species by establishing positive plant-soil feedback. The strong adaptation and assimilative capacity contributed to D. angustifolia encroaching in the alpine tundra. Our research indicates that D. angustifolia significantly impacts the rhizosphere soil microbial of the alpine tundra.

Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere?

Plant evolutionary history influences the taxonomic composition of the root-associated bacterial community, but whether it can also modulate its functioning is unknown. Here, we tested the hypothesis that crop diversification is a significant factor determining the ecology of the functional group of nitrogen-fixing bacteria the rhizosphere of Poaceae. A greenhouse experiment was carried out using a range of Poaceae, i.e. four Zea mays varieties (from two genetic groups) and teosinte (representing maize’s ancestor), sorghum (from the same Panicoideae subfamily), and wheat (from neighboring Pooideae subfamily), as well as the dicot tomato as external reference. Diazotroph rhizosphere community was characterized at 21 days in terms of size (quantitative PCR of nifH genes), composition (T-RFLP and partial sequencing of nifH alleles) and functioning (quantitative RT-PCR, T-RFLP and partial sequencing of nifH transcripts). Plant species and varieties had a significant effect on diazotroph community size and the number of nifH transcripts per root system. Contrarily to expectations, however, there was no relation between Poaceae evolutionary history and the size, diversity or expression of the rhizosphere diazotroph community. These results suggest a constant selection of this functional group through evolution for optimization of nitrogen fixation in the rhizosphere.

Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth

Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.

Influence of edaphic and management factors on the diversity and abundance of ammonia-oxidizing thaumarchaeota and bacteria in soils of bioenergy crop cultivars

Ammonia-oxidizing thaumarcheota (AOA) and ammonia-oxidizing bacteria (AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene (amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass (Panicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. Nitrosotalea-like and Nitrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with Nitrososphaera and Nitrosospira cluster 3A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses.

Xander: employing a novel method for efficient gene-targeted metagenomic assembly

BACKGROUND

Metagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes.

RESULTS

We present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences.

CONCLUSION

Xander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.

Linking DNRA community structure and activity in a shallow lagoonal estuarine system

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between the structure and activity of DNRA communities has yet to be discovered. We examined the composition, diversity, abundance, and activities of DNRA communities at five sites along a salinity gradient in the New River Estuary, North Carolina, USA, a shallow temporal/lagoonal estuarine system. Sediment slurry incubation experiments with (15)N-nitrate were conducted to measure potential DNRA rates, while the abundance of DNRA communities was calculated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, commonly found in DNRA bacteria. A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine the diversity and composition of DNRA communities within the estuarine sediment community. We found higher levels of nrfA gene abundance and DNRA activities in sediments with higher percent organic content. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the salinity gradient of the New River Estuary. Percent abundance of dominant populations was found to have significant influence on overall activities of DNRA communities. Abundance of dominant DNRA bacteria and organic carbon availability are important regulators of DNRA activities in the eutrophic New River Estuary.

Shifts in the microbial community, nitrifiers and denitrifiers in the biofilm in a full-scale rotating biological contactor

The objective of this study was to investigate the microbial community shifts, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath. The microbial consortia were profiled using multiple approaches, including 454 high-throughput sequencing of the V3-V4 region of 16S rRNA gene, clone libraries, and quantitative polymerase chain reaction (qPCR). The results demonstrated that (1) the overall microbial community at different locations had distinct patterns, that is, there were similar microbial communities at the beginnings of the two RBC trains and completely different populations at the ends of the two RBC trains; (2) nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira), increased in relative abundance in the biofilm along the flowpath, whereas denitrifiers (Rhodanobacter, Paracoccus, Thauera, and Azoarcus) markedly decreased; (3) the AOA were subdominant to the AOB in all sampled sections; and (4) strong ecological associations were shown among different bacteria. Overall, the results of this study provided more comprehensive information regarding the biofilm community composition and assemblies in full-scale RBCs.

Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass (Panicum virgatum L.) through root exudates

Identification of microbes that actively utilize root exudates is essential to understand plant-microbe interactions. To identify active root exudate-utilizing microorganisms associated with switchgrass - a potential bioenergy crop - plants were labelled in situ with (13) CO2 , and 16S and 18S rRNA genes in the (13) C-labelled rhizosphere DNA were pyrosequenced. Multi-pulse labelling for 5 days produced detectable (13) C-DNA, which was well separated from unlabelled DNA. Methylibium from the order Burkholderiales were the most heavily labelled bacteria. Pythium, Auricularia and Galerina were the most heavily labelled eukaryotic microbes. We also identified a Glomus intraradices-like species; Glomus members are arbuscular mycorrhizal fungi that are able to colonize the switchgrass root. All of these heavily labelled microorganisms were also among the most abundant species in the rhizosphere. Species belonging to Methylibium and Pythium were the most heavily labelled and the most abundant bacteria and eukaryotes in the rhizosphere of switchgrass. Our results revealed that nearly all of the dominant rhizosphere bacterial and eukaryotic microbes were able to utilize root exudates. The enrichment of microbial species in the rhizosphere is selective and mostly due to root exudation, which functions as a nutrition source, promoting the growth of these microbes.

Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior

Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b) where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a) and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA) showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.

An affinity-effect relationship for microbial communities in plant-soil feedback loops

Feedback loops involving soil microorganisms can regulate plant populations. Here, we hypothesize that microorganisms are most likely to play a role in plant-soil feedback loops when they possess an affinity for a particular plant and the capacity to consistently affect the growth of that plant for good or ill. We characterized microbial communities using whole-community DNA fingerprinting from multiple "home-and-away" experiments involving giant ragweed (Ambrosia trifida L.) and common sunflower (Helianthus annuus L.), and we looked for affinity-effect relationships in these microbial communities. Using canonical ordination and partial least squares regression, we developed indices expressing each microorganism's affinity for ragweed or sunflower and its putative effect on plant biomass, and we used linear regression to analyze the relationship between microbial affinity and effect. Significant linear affinity-effect relationships were found in 75 % of cases. Affinity-effect relationships were stronger for ragweed than for sunflower, and ragweed affinity-effect relationships showed consistent potential for negative feedback loops. The ragweed feedback relationships indicated the potential involvement of multiple microbial taxa, resulting in strong, consistent affinity-effect relationships in spite of large-scale microbial variability between trials. In contrast, sunflower plant-soil feedback may involve just a few key players, making it more sensitive to underlying microbial variation. We propose that affinity-effect relationship can be used to determine key microbial players in plant-soil feedback against a low "signal-to-noise" background of complex microbial datasets.