03041nas a2200373   4500008004100000245008800041210006900129300001400198490000600212520192100218653001602139653002202155653001602177653002002193100002702213700001902240700002102259700002402280700002602304700002102330700001802351700002302369700001802392700001802410700001702428700002302445700002102468700002002489700002702509700002002536700002302556700002302579856006502602       2019                        eng d00aMetaphenomic response of a native prairie soil microbiome to moisture perturbations0 aMetaphenomic response of a native prairie soil microbiome to moi  ae00061-190 v43 a<p>Climate change is causing shifts in precipitation patterns in the central grasslands of the United States, with largely unknown consequences on the collective physiological responses of the soil microbial community, i.e., the metaphenome. Here, we used an untargeted omics approach to determine the soil microbial community&rsquo;s metaphenomic response to soil moisture and to define specific metabolic signatures of the response. Specifically, we aimed to develop the technical approaches and metabolic mapping framework necessary for future systematic ecological studies. We collected soil from three locations at the Konza Long-Term Ecological Research (LTER) field station in Kansas, and the soils were incubated for 15 days under dry or wet conditions and compared to field-moist controls. The microbiome response to wetting or drying was determined by 16S rRNA amplicon sequencing, metatranscriptomics, and metabolomics, and the resulting shifts in taxa, gene expression, and metabolites were assessed. Soil drying resulted in significant shifts in both the composition and function of the soil microbiome. In contrast, there were few changes following wetting. The combined metabolic and metatranscriptomic data were used to generate reaction networks to determine the metaphenomic response to soil moisture transitions. Site location was a strong determinant of the response of the soil microbiome to moisture perturbations. However, some specific metabolic pathways changed consistently across sites, including an increase in pathways and metabolites for production of sugars and other osmolytes as a response to drying. Using this approach, we demonstrate that despite the high complexity of the soil habitat, it is possible to generate insight into the effect of environmental change on the soil microbiome and its physiology and functions, thus laying the groundwork for future, targeted studies.</p>10ametaphenome10ametatranscriptome10amulti-omics10asoil microbiome1 aChowdhury, Taniya, Roy1 aLee, Joon-Yong1 aBottos, Eric, M.1 aBrislawn, Colin, J.1 aWhite, Richard, Allen1 aBramer, Lisa, M.1 aBrown, Joseph1 aZucker, Jeremy, D.1 aKim, Young-Mo1 aJumpponen, A.1 aRice, C., W.1 aFansler, Sarah, J.1 aMetz, Thomas, O.1 aMcCue, Lee, Ann1 aCallister, Stephen, J.1 aSong, Hyun-Seob1 aJansson, Janet, K.1 aHallam, Steven, J.  uhttp://msystems.asm.org/lookup/doi/10.1128/mSystems.00061-1903068nas a2200349   4500008004100000245014000041210006900181300000900250490000600259520197400265653001702239653001902256653002002275653001702295653001902312653001902331653002002350100002402370700002202394700002302416700002602439700001902465700001602484700002502500700001702525700002302542700001702565700002502582700002202607700002302629856006602652       2018                        eng d00aMicrobial community structure and functional potential in cultivated and native tallgrass prairie soils of the midwestern united states0 aMicrobial community structure and functional potential in cultiv  a17750 v93 a<p>The North American prairie covered about 3.6 million-km<sup>2</sup> of the continent prior to European contact. Only 1&ndash;2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices &ndash; perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.</p>10acarbon cycle10aClimate change10aLand management10ametagenomics10anative prairie10anitrogen cycle10asoil microbiome1 aMackelprang, Rachel1 aGrube, Alyssa, M.1 aLamendella, Regina1 aJesus, Ederson, da C.1 aCopeland, Alex1 aLiang, Chao1 aJackson, Randall, D.1 aRice, C., W.1 aKapucija, Stefanie1 aParsa, Bayan1 aTringe, Susannah, G.1 aTiedje, James, M.1 aJansson, Janet, K.  uhttps://www.frontiersin.org/articles/10.3389/fmicb.2018.01775