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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Evaluating the Impact of Atmospheric Depositions on Springtime Dinitrogen Fixation in the Cretan Sea (Eastern Mediterranean)—A Mesocosm Approach
Eyal Rahav,Eyal Rahav,Cheung Shun-Yan,Guo Cui,Hongbin Liu,Tatiana M. Tsagaraki,Antonia Giannakourou,Anastasia Tsiola,Stella Psarra,Anna Lagaria,Margaret R. Mulholland,Eleni Stathopoulou,Pitta Paraskevi,Barak Herut,Ilana Berman-Frank +14 more
TL;DR: In this paper, the authors studied the impact of the atmospheric deposition of dust and aerosols on N2 fixation in the Cretan Sea (Eastern Mediterranean Sea) and found that mixed polluted aerosols and Saharan dust (hereafter SD) were added to nine mesocosms (3-m3 each) containing surface mixed layer seawater (~10 m).
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Combined effects of elevated CO2, N fertilizer and water deficit stress on diazotrophic community in sub-humid tropical paddy soil
TL;DR: In this paper, a study was conducted in CO2-maintained open-top chamber to assess the diazotrophic community under combined influence of carbon dioxide (eCO2) and water deficit stress (WDS) for rice.
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Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary.
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High-throughput analysis of anammox bacteria in wetland and dryland soils along the altitudinal gradient in Qinghai-Tibet Plateau.
TL;DR: It was the small‐scale environmental heterogeneities between wetland and dryland soils that determined the biogeographical distribution of anammox bacteria and their diversity, community composition, and abundance did not show significant variation with altitude at large scale.
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Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions.
Hirotsugu Fujitani,Manami Nomachi,Yu Takahashi,Yoshiaki Hasebe,Masahiro Eguchi,Satoshi Tsuneda +5 more
TL;DR: This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
Species assemblages and indicator species:the need for a flexible asymmetrical approach
Marc Dufrêne,Pierre Legendre +1 more
TL;DR: A new and simple method to find indicator species and species assemblages characterizing groups of sites, and a new way to present species-site tables, accounting for the hierarchical relationships among species, is proposed.
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