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The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).

New technologies have enabled researchers to peer into the ‘black box’ of freshwater bacterial community structure. Inland waters are home to an assemblage of bacteria that is distinct from terrestrial and marine communities, and the various freshwater bacterial groups have distinctive lifestyles and habitat distributions. These bacteria form communities that are highly diverse but tend to be dominated by a few species at any given time. The identity of the dominants can change rapidly in relation to changing environmental conditions and biological interactions. Some of the important environmental factors that have been shown to structure lake bacterial communities include temperature, oxygen concentration, water clarity, pH, humic acid content, salinity, nutrient concentration, water column mixing, water residence time, and toxic metals. The influence of these factors defines changing patterns in bacterial community composition in space and time. Bacterial communities are also structured by biological interactions such as competition, predation by nanoflagellate grazers and zooplankton, viral lysis, and linkages to algae. Under the influence of these structuring forces, bacterial dynamics suggest communities in varying states of recovery from ecological disturbances that may serve to maintain the high diversity of freshwater bacterial communities.

Utilization of dissolved organic matter (DOM) is thought to be the purview of heterotrophic microorganisms, but photoautotrophs can take up dissolved organic nitrogen (DON) and dissolved organic carbon (DOC). This study investigated DOC and DON uptake in a laminated cyanobacterial mat community from hypersaline Salt Pond (San Salvador, Bahamas). The total community uptake of (3)H-labeled substrates was measured in the light and in the dark and under conditions of high and low salinity. Salinity was the primary control of DOM uptake, with increased uptake occurring under low-salinity, 'freshened' conditions. DOC uptake was also enhanced in the light as compared with the dark and in samples incubated with the photosystem II inhibitor 3(3,4-dichlorophenyl)-1, 1-dimethylurea, suggesting a positive association between photosynthetic activity and DOC uptake. Microautoradiography revealed that some DOM uptake was attributed to cyanobacteria. Cyanobacteria DOM uptake was negatively correlated with that of smaller filamentous microorganisms, and DOM uptake by individual coccoid cells was negatively correlated with uptake by colonial coccoids. These patterns of activity suggest that Salt Pond microorganisms are engaged in resource partitioning, and DOM utilization may provide a metabolic boost to both heterotrophs and photoautrophs during periods of lowered salinity.

This study examined the similarity of epilimnetic bacterial community composition (BCC) across several within- and among-lake spatial scales, and the environmental factors giving rise to similar bacterial communities in different lakes were also explored. Samples were collected from 13 northern and southern Wisconsin lakes representing gradients in lake size, productivity, dissolved organic carbon and humic acid contents, and pH. Hypotheses regarding patchy distribution of bacterial communities in lakes were tested by comparing samples collected from nearby (tens of meters) and distant (hundreds of meters) sampling sites in the same lake. BCC was characterized by using a molecular fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA). Overall, samples collected at the 10-m, 100-m, and between-lake scales differed by 13, 17, and 75%, respectively. Variation at these last two scales was significant. The development of within-lake variation in BCC appeared to depend on the isolation of water by lake shoreline features such as bays or narrow constrictions. ARISA profiles from northern lakes had fewer peaks and were less similar to each other than were those of the southern lakes, suggesting that regional features do not necessarily lead to the development of similar bacterial communities. Lakes at similar positions on productivity and dissolved organic carbon concentration gradients had similar bacterial communities, and bacterial diversity was positively correlated with lake productivity and water temperature. Factorial studies taking into account these gradients, as well as regional spatial scales, should provide much insight into the nature of aquatic bacterial biogeography.

Bacterioplankton community composition (BCC) was monitored in a shallow humic lake in northern Wisconsin, USA, over 3 years using automated ribosomal intergenic spacer analysis (ARISA). Comparison of ARISA profiles of bacterial communities over time indicated that BCC was highly variable on a seasonal and annual scale. Nonmetric multidimensional scaling (MDS) analysis indicated little similarity in BCC from year to year. Nevertheless, annual patterns in bacterioplankton community diversity were observed. Trends in bacterioplankton community diversity were correlated to annual patterns in community succession observed for phytoplankton and zooplankton populations, consistent with the notion that food web interactions affect bacterioplankton community structure in this humic lake. Bacterioplankton communities experience a dramatic drop in richness and abundance each year in early summer, concurrent with an increase in the abundance of both mixotrophic and heterotrophic flagellates. A second drop in richness, but not abundance, is observed each year in late summer, coinciding with an intense bloom of the nonphagotrophic dinoflagellate Peridinium limbatum. A relationship between bacterial community composition, size, and abundance and the population dynamics of Daphnia was also observed. The noted synchrony between these major population and species shifts suggests that linkages across trophic levels play a role in determining the annual time course of events for the microbial and metazoan components of the plankton.

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

Species richness and species diversity of bacterioplankton, phytoplankton and protoplankton were examined in Crystal Bog, a humic lake in northern Wisconsin, as part of an NSF sponsored Microbial Observatory Program. Crystal Bog is part of the North Temperate Lakes Long-Term Ecological Research site. Automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterial diversity. Phytoplankton and protoplankton were enumerated in a settling chamber with an inverted microscope. Four distinct phases in the ice-free season of the bog can be recognized based on microbial populations. The first phase extends from ice-out until about the first week of April. During this phase three species of dinoflagellates come to dominate the phytoplankton, with Glenodinium quadridens representing 60% of total phytoplankton biovolume. By mid-April the spring dinoflagellate blooms collapse. The second phase is a period of instability as a series of species dominates the phytoplankton. In mid-July dinoflagellates again dominate the third phase, and Peridinium limbatum alone represents 90% of the bog phytoplankton. The fourth phase is a stable period as P. limbatum slowly declines in late summer and fall. A strong correlation was found between bacterial and phytoplankton diversity (Shannon–Weaver Index) in this bog, suggesting the two microbial communities are linked. The protoplankton, however, were relatively uniform throughout the ice-free period. The ice-covered period may be treated as a fifth phase. When snow accumulates over the ice-covered bog, light penetration is blocked and photosynthesis shut off. Heterotrophic protozoa assume dominance in the plankton.

Sustaining soil productivity in agricultural systems presents a fundamental agroecological challenge: nutrient provisioning depends upon aggregate turnover and microbial decomposition of organic matter (SOM); yet to prevent soil depletion these processes must be balanced by those that restore nutrients and SOM (soil building processes). These nutrient provisioning and soil building processes are inherently in conflict; management practices that create spatial separation between them may enable each to occur effectively within a single growing season, thereby supporting high crop yield while avoiding soil depletion. Soil functional zone management (SFZM), an understudied but increasingly adopted strategy for annual row-crop production, may help meet this agroecological challenge by creating spatial heterogeneity in biophysical conditions between crop rows and inter-rows. However, the process-level effects of this spatial heterogeneity on nutrient provisioning and soil building processes have not been characterised. We assessed the magnitude and spatial distribution of nutrient provisioning and soil building processes in model SFZM (ridge tillage) and conventional tillage (chisel plough) systems in four US states encompassing a major global agricultural production region. For soil building we measured bulk density, aggregation and permanganate oxidisable carbon (POXC); for nutrient provisioning we measured microbial decomposition activity, nutrient mineralisation and plant-available nitrogen. After two years, POXC increased under ridge tillage (0–20cm depth) compared with chisel plough. Ridge tillage also enhanced nutrient provisioning processes in crop rows, increasing plant-available nitrogen in synchrony with maize peak nitrogen demand. Structural equation modelling revealed that improvement in soil building processes under ridge tillage caused rapid enhancement of nutrient provisioning processes in SOM-poor soils. Increases in crop row POXC stimulated microbial decomposition activity, which was associated with increased plant-available nitrogen during the phase of maize peak nitrogen demand. The decimetre-scale spatial heterogeneity created by ridge tillage enables reconciliation of nutrient provisioning and soil building processes in row-crop agroecosystems. In doing so, ridge tillage promotes critical soil processes necessary for increasing the range of ecosystem services provided by intensive production systems. SFZM approaches may have particular value in regions with SOM-poor soils, which would benefit from rapid increases in surface organic carbon. Also, by concentrating and promoting nutrient provisioning processes around crop roots during crop peak nitrogen demand, ridge tillage may enhance nitrogen-use efficiency and reduce current fertiliser requirements.

Background and Aims Lespedeza cuneata (Dum. Cours.) G. Don is an invasive legume that displaces populations of native N. American congeners. Our aims are to determine the growth benefits of different rhizobacterial strains for L. cuneata and native Lespedeza virginica (L.) Britton, and to determine if these strains influence competition between these plants.

The objective of this study is to understand how soil microorganisms interact with cover crop-derived allelochemicals to suppress weed germination and growth following cover crop residue incorporation. We conducted a time series experiment crossing sterilized and non-sterilized soil with four different residue treatments. We measured weed seed germination rates, radicle elongation, and disease incidence in seed germination bioassays. We also monitored cover crop-derived, isoflavone allelochemicals in these bioassays. We partitioned the total weed suppression into three sources: microbe-only inhibition, residue-only inhibition, and the microbe-residue interaction. Microbial activity suppressed weed germination and growth for 30 days, while cover crop-derived allelochemicals provided suppression for a limited time. There was an antagonistic interaction between microbes and allelochemicals. This interaction was strongest for water-soluble allelochemicals, while residue fractions containing intact plant tissues retained greater suppressiveness even in the presence of a live microbial community. Microbial activity can directly suppress weed germination and growth, but microorganisms also indirectly help weeds by degrading cover crop-derived allelochemicals. As a result of these interactions, cover crop-derived weed suppression in agricultural soils shifts from an early allelochemical-dominated phase to a later phase where microbial suppression is more important.