Genome sequences of spp. CF3062 and CF3016 isolated from nodules found on herbarium specimens collected in 2004 and 2015.

We present the genomes of two isolates isolated from nodules found on herbarium specimens at the Marion Ownbey Herbarium at Washington State University. These genomes and others from herbarium specimens offer an unprecedented opportunity to study the bacterial evolution of plant-associated microbes over long time scales.

Prairie soil improves wheat establishment and accelerates the developmental transition to flowering compared to agricultural soils.

Less than 1% of native prairie lands remain in the United States. Located in eastern Washington, the rare habitat called Palouse prairie was largely converted to wheat monocropping. With this conversion came numerous physical, chemical, and biological changes to the soil that may ultimately contribute to reduced wheat yields.

Back to the future: Using herbarium specimens to isolate nodule-associated bacteria.

Herbarium specimens are increasingly being used as sources of information to understand the ecology and evolution of plants and their associated microbes. Most studies have used specimens as a source of genetic material using culture-independent approaches. We demonstrate that herbarium specimens can also be used to culture nodule-associated bacteria, opening the possibility of using specimens to understand plant-microbe interactions at new spatiotemporal scales.

NFDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs.

Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase () is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase () and (iii) iron nitrogenase (). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist.

MerCat2: a versatile -mer counter and diversity estimator for database-independent property analysis obtained from omics data.

Motivation: MerCat2 ("Mer-Catenate2") is a versatile, parallel, scalable and modular property software package for robustly analyzing features in omics data. Using massively parallel sequencing raw reads, assembled contigs, and protein sequences from any platform as input, MerCat2 performs -mer counting of any length , resulting in feature abundance counts tables, quality control reports, protein feature metrics, and graphical representation (i.e.

The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.

Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics.

Regional biogeography versus intra-annual dynamics of the root and soil microbiome.

Background: Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs.

Negotiating mutualism: A locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts.

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment.

Electrochemically Active Biofilms as an Indicator of Soil Health.

Soil health is a complex phenomenon that reflects the ability of soil to support both plant growth and other ecosystem functions. To our knowledge, research on extracellular electron transfer processes in soil environments is limited and could provide novel knowledge and new ways of monitoring soil health. Electrochemical activities in the soil can be studied by inserting inert electrodes.

Multiple Mutualism Effects generate synergistic selection and strengthen fitness alignment in the interaction between legumes, rhizobia and mycorrhizal fungi.

Nearly all organisms participate in multiple mutualisms, and complementarity within these complex interactions can result in synergistic fitness effects. However, it remains largely untested how multiple mutualisms impact eco-evolutionary dynamics in interacting species. We tested how multiple microbial mutualists-N-fixing bacteria and mycorrrhizal fungi-affected selection and heritability of traits in their shared host plant (Medicago truncatula), as well as fitness alignment between partners.

An experimental test of stabilizing forces in the field niche.

Modern coexistence theory holds that stabilizing mechanisms, whereby species limit the growth of conspecifics more than that of other species, are necessary for species to coexist. Here, we used experimental and observational approaches to assess stabilizing forces in eight locally co-occurring, annual, legume species in the genus Trifolium. We experimentally measured self-limitation in the field by transplanting Trifolium species into each other's field niches while varying competition and related these patterns to the field coexistence dynamics of natural Trifolium populations.

Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms.

Evolutionary biologists typically envision a trait's genetic basis and fitness effects occurring within a single species. However, traits can be determined by and have fitness consequences for interacting species, thus evolving in multiple genomes. This is especially likely in mutualisms, where species exchange fitness benefits and can associate over long periods of time.

Decreased coevolutionary potential and increased symbiont fecundity during the biological invasion of a legume-rhizobium mutualism.

Although most invasive species engage in mutualism, we know little about how mutualism evolves as partners colonize novel environments. Selection on cooperation and standing genetic variation for mutualism traits may differ between a mutualism's invaded and native ranges, which could alter cooperation and coevolutionary dynamics. To test for such differences, we compare mutualism traits between invaded- and native-range host-symbiont genotype combinations of the weedy legume, Medicago polymorpha, and its nitrogen-fixing rhizobium symbiont, Ensifer medicae, which have coinvaded North America.

Microbial Inoculants: Silver Bullet or Microbial Jurassic Park?

The appeal of using microbial inoculants to mediate plant traits and productivity in managed ecosystems has increased over the past decade, because microbes represent an alternative to fertilizers, pesticides, and direct genetic modification of plants. Using microbes bypasses many societal and environmental concerns because microbial products are considered a more sustainable and benign technology. In our desire to harness the power of plant-microbial symbioses, are we ignoring the possibility of precipitating microbial invasions, potentially setting ourselves up for a microbial Jurassic Park? Here, we outline potential negative consequences of microbial invasions and describe a set of practices (Testing, Regulation, Engineering, and Eradication, TREE) based on the four stages of invasion to prevent microbial inoculants from becoming invasive.

Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function.

Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear.

Social Evolution and Cheating in Plant Pathogens.

Plant pathogens are a critical component of the microbiome that exist as populations undergoing ecological and evolutionary processes within their host. Many aspects of virulence rely on social interactions mediated through multiple forms of public goods, including quorum-sensing signals, exoenzymes, and effectors. Virulence and disease progression involve life-history decisions that have social implications with large effects on both host and microbe fitness, such as the timing of key transitions.

A Genome Resource for the Apple Powdery Mildew Pathogen .

Powdery mildew, caused by , is an economically important disease of apple and pear trees. A single monoconidial strain (PuE-3) of this biotrophic fungus was used to extract DNA for Illumina sequencing. Data were assembled to form a draft genome of 43.

Legumes Modulate Allocation to Rhizobial Nitrogen Fixation in Response to Factorial Light and Nitrogen Manipulation.

The costs and benefits that define gain from trade in resource mutualisms depend on resource availability. Optimal partitioning theory predicts that allocation to direct uptake trade will be determined by both the relative benefit of the resource acquired through trade and the relative cost of the resource being traded away. While the costs and benefits of carbon:nitrogen exchange in the legume-rhizobia symbiosis have been examined in depth with regards to mineral nitrogen availability, the effects of varying carbon costs are rarely considered.

Rapid evolution of during invasion shifts interactions with the soybean looper.

The Enemy Release Hypothesis posits that invasion of novel habitats can be facilitated by the absence of coevolved herbivores. However, a new environment and interactions with unfamiliar herbivores may impose selection on invading plants for traits that reduce their attractiveness to herbivores or for enhanced defenses compared to native host plants, leading to a pattern similar to enemy release but driven by evolutionary change rather than ecological differences. The Shifting Defense Hypothesis posits that plants in novel habitats will shift from specialized defense mechanisms to defense mechanisms effective against generalist herbivores in the new range.

Revealing the Draft Genome Sequence of sp. Strain USDA 3458, an Effective Symbiotic Diazotroph Isolated from Cowpea () Genotype IT82E-16.

Pairing plants with plant growth-promoting bacteria is critical to the future of agriculture. sp. strain USDA 3458 isolated from (cowpea) paired with cowpea genotype IT82E-16 represents a novel combination in arid regions.

Elucidation of the Genome of Bradyrhizobium sp. Strain USDA 3456, a Historic Agricultural Diazotroph from Cowpea (Vigna unguiculata).

sp. strain USDA 3456 is a historic strain from the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) National Germplasm Collection isolated from (cowpea) in 1966. Strain USDA 3456 has been utilized in global agricultural applications, including improving soil nitrogen fertility.

Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus.

Background: A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain predicted transcripts. A similarity search algorithm is then applied to a related organism to infer possible function of these predicted transcripts. While some of these predictions may be inaccurate and transcripts with low coverage are often missed, we observe that it is possible to obtain a more complete set of transcripts to facilitate possible functional assignments by starting the search from the intermediate de Bruijn graph that contains all branching possibilities.