Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool
Qiong Wang,John F. Quensen,Jordan A. Fish,Tae Kwon Lee,Yanni Sun,James M. Tiedje,James R. Cole +6 more
TLDR
To accurately detect and correct frameshifts caused by indel sequencing errors, FrameBot was developed, a tool for frameshift correction and nearest-neighbor classification, and its accuracy was compared to that of two other rapid frameshIFT correction tools.Abstract:
Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase ( nifH ). We obtained 1.1 million nifH 454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all nifH reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those nifH sequences related to the Proteobacteria phylum were most abundant, followed by those for Cyanobacteria in the Alaska and Utah sites. Predominant genera with nifH sequences similar to reads included Azospirillum , Bradyrhizobium , and Rhizobium , the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known nifH gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any. IMPORTANCE High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more straightforward to assess the genes directly responsible for the ecological function (ecofunctional genes). However, analyzing these genes involves technical challenges beyond those seen for rRNA. In particular, frameshift errors cause garbled downstream protein translations. Our FrameBot tool described here both corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences. We validated this new tool with sequences from defined communities and demonstrated the tool’s utility on nifH gene fragments sequenced from soils in well-characterized and major terrestrial ecosystem types.read more
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The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea.
Yanying Zhang,Yanying Zhang,Qingsong Yang,Juan Ling,Joy D. Van Nostrand,Zhou Shi,Jizhong Zhou,Junde Dong +7 more
TL;DR: The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazOTrophs play an important role in the nitrogen cycle of the coral holobiont.
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Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents.
Sanni L. Aalto,Sanni L. Aalto,Jatta Saarenheimo,Anu Mikkonen,Antti J. Rissanen,Marja Tiirola +5 more
TL;DR: The results suggest that although future climate‐change‐driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.
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Transportation of Diazotroph Community From the Upstream to Downstream of the Kuroshio
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Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function.
TL;DR: Assessment of structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites demonstrates that root- associated diaztrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazOTrophic community by switchgrass roots.
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nir gene-based co-occurrence patterns reveal assembly mechanisms of soil denitrifiers in response to fire.
Marta Goberna,Santiago Donat,Eduardo Pérez-Valera,Eduardo Pérez-Valera,Sara Hallin,Miguel Verdú +5 more
TL;DR: A framework to analyse the co-existence of denitrifiers across multiple assemblages by using nir gene-based co-occurrence networks is proposed and applied in Mediterranean soils before and during one year after an experimental fire.
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