01833nas a2200253   4500008004100000245012200041210006900163490001300232520105900245100001601304700001401320700001601334700001201350700001901362700001601381700002001397700001701417700001801434700001501452700001501467700001901482700001801501856006001519       2014                        eng d00aFOAM: Functional Ontology Assignments for Metagenomes: a Hidden Markov  Model (HMM) database with environmental focus0 aFOAM Functional Ontology Assignments for Metagenomes a Hidden Ma0 v42: e1453 a<p>A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. &lsquo;profiles&rsquo;) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.</p>1 aPrestat, E.1 aDavid, M.1 aHultman, J.1 aTas, N.1 aLamendella, R.1 aDvornik, J.1 aMackelprang, R.1 aMyrold, D.D.1 aJumpponen, A.1 aTringe, S.1 aHolman, E.1 aMavromatis, K.1 aJansson, J.K.  uhttps://academic.oup.com/nar/article/42/19/e145/290247903323nas a2200217   4500008004100000245012400041210006900165300001500234490000700249520261700256100002202873700002002895700001802915700001702933700001502950700001702965700001602982700001602998700001703014856007403031       2013                        eng d00aAltered precipitation regime affects the function and composition of soil microbial communities on multiple time scales0 aAltered precipitation regime affects the function and compositio  a2334 -23450 v943 a<p>Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting &ldquo;Ambient&rdquo; and &ldquo;Altered&rdquo; (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = &minus;0.01 and &minus;0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 &plusmn; 0.03 &gt; 0.46 &plusmn; 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (β-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal : bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.</p>1 aZeglin, Lydia, H.1 aBottomley, P.J.1 aJumpponen, A.1 aRice, C., W.1 aArango, M.1 aLindsley, A.1 aMcGowan, A.1 aMfombep, P.1 aMyrold, D.D.  uhttps://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-2018.100790nas a2200241   4500008004100000245009700041210006900138300001000207490000800217100001800225700002200243700001400265700001600279700001400295700001600309700001700325700001600342700001600358700001700374700001500391700001700406856012500423       2013                        eng d00aFungal community responses to discrete precipitation pulses under altered rainfall intervals0 aFungal community responses to discrete precipitation pulses unde  a182 -0 v1031 aJumpponen, A.1 aZeglin, Lydia, H.1 aDavid, M.1 aPrestat, E.1 aBrown, S.1 aDvornik, J.1 aLothamer, K.1 aHettich, R.1 aJansson, J.1 aRice, C., W.1 aTringe, S.1 aMyrold, D.D.  uhttp://knz.lternet.edu/content/fungal-community-responses-discrete-precipitation-pulses-under-altered-rainfall-intervals