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
Citations
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Retrieved 16S rRNA and nifH sequences reveal co-dominance of Bradyrhizobium and Ensifer (Sinorhizobium) strains in field-collected root nodules of the promiscuous host Vigna radiata (L.) R. Wilczek.
Sughra Hakim,Sughra Hakim,Babur S. Mirza,Ahmad Zaheer,Ahmad Zaheer,Joan E. McLean,Asma Imran,Asma Imran,Sumera Yasmin,Sumera Yasmin,M. Sajjad Mirza,M. Sajjad Mirza +11 more
TL;DR: Co-dominance of Bradyrhizobium and Ensifer strains in the nodules of mung bean indicates the potential role of the host plant in selecting specific endophytic rhizobial populations, and identifies the presence of several non-rhizobials from phyla Proteobacteria, Actinob bacteria, Bacteroides and Firmicutes.
Journal ArticleDOI
Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils
Christopher Ryan Penton,Christopher Ryan Penton,Derek St. Louis,Amanda Pham,James R. Cole,Liyou Wu,Yiqi Luo,Edward A. G. Schuur,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou,James M. Tiedje +11 more
TL;DR: The N functional microbial communities of the prairie were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ, while the AK permafrost communities showed decreased richness and a structural change only with the nirK-harboring bacterial community.
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Atmospheric Methane Oxidizers Are Dominated by Upland Soil Cluster Alpha in 20 Forest Soils of China
TL;DR: This study suggests that combining the deep sequencing of 16S rRNA and pmoA genes to characterize MOB in forest soils is the best choice.
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Ammonia-oxidizing bacteria are sensitive and not resilient to organic amendment and nitrapyrin disturbances, but ammonia-oxidizing archaea are resistant
TL;DR: In this paper, the authors explored the responses of the AOA and AOB communities after disturbances caused by the application of inorganic N (urea alone, IN), an organic amendment (cattle manure, OA), a urease inhibitor (NBPT) and a nitrification inhibitor (nitrapyrin) or their combination in a calcareous soil after 85 days.
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Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients.
TL;DR: This paper presents a probabilistic analysis of the response of E. coli to high-resolutionresolution X-ray diffraction analysis of Na6(CO3)(SO4)– Na2SO4, a type of “ghost oil” found in the mantle of the North Atlantic Ocean.
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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