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      Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China

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          Abstract

          Bacteria are the highest abundant microorganisms in the soil. To investigate bacteria community structures, diversity, and functions, contrasting them in four different seasons all the year round with/within two different forest type soils of China. We analyzed soil bacterial community based on 16S rRNA gene sequencing via Illumina HiSeq platform at a temperate deciduous broad-leaved forest (Baotianman, BTM) and a tropical rainforest (Jianfengling, JFL). We obtained 51,137 operational taxonomic units (OTUs) and classified them into 44 phyla and 556 known genera, 18.2% of which had a relative abundance >1%. The composition in each phylum was similar between the two forest sites. Proteobacteria and Acidobacteria were the most abundant phyla in the soil samples between the two forest sites. The Shannon index did not significantly differ among the four seasons at BTM or JFL and was higher at BTM than JFL in each season. The bacteria community at both BTM and JFL showed two significant ( P < 0.05) predicted functions related to carbon cycle (anoxygenic photoautotrophy sulfur oxidizing and anoxygenic photoautotrophy) and three significant ( P < 0.05) predicted functions related to nitrogen cycle (nitrous denitrificaton, nitrite denitrification, and nitrous oxide denitrification). We provide the basis on how changes in bacterial community composition and diversity leading to differences in carbon and nitrogen cycles at the two forests.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          T. Magoc, S. L. Salzberg (2013)
          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            The diversity and biogeography of soil bacterial communities.

            Noah Fierer, Robert B Jackson (2006)
            For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.
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              Pyrosequencing enumerates and contrasts soil microbial diversity.

              Luiz Roesch, Roberta R Fulthorpe, Alberto Riva … (2007)
              Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26,140 to 53,533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52,000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%-12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.
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                Author and article information

                Contributors
                Journal
                Journal ID (nlm-ta): Front Microbiol
                Journal ID (iso-abbrev): Front Microbiol
                Journal ID (publisher-id): Front. Microbiol.
                Title: Frontiers in Microbiology
                Publisher: Frontiers Media S.A.
                ISSN (Electronic): 1664-302X
                Publication date (Electronic): 31 July 2018
                Publication date Collection: 2018
                Volume: 9
                Electronic Location Identifier: 1693
                Affiliations
                [1] 1Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University , Yangling, China
                [2] 2Medical College, Baoji Vocational Technology College , Baoji, China
                [3] 3Départment des Sciences Biologiques, Institut des Sciences de l'Environnement, Université du Québec à Montréal , Montreal, QC, Canada
                [4] 4Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry , Beijing, China
                [5] 5Baotianman Natural Reserve Administration , Neixiang, China
                [6] 6Research Institute of Tropical Forestry, Chinese Academy of Forestry , Guangzhou, China
                [7] 7State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University , Changchun, China
                Author notes

                Edited by: Malin Bomberg, VTT Technical Research Centre of Finland Ltd, Finland

                Reviewed by: Nicole Sukdeo, University of Northern British Columbia, Canada; Caitlin Looby, University of Denver, United States

                *Correspondence: Changhui Peng peng.changhui@ 123456uqam.ca

                This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology

                Article
                DOI: 10.3389/fmicb.2018.01693
                PMC ID: 6080587
                PubMed ID: 30108560
                SO-VID: 01be0e0a-4578-470b-95ba-62f9e43c9d68
                Copyright © Copyright © 2018 Wei, Peng, Yang, Song, Li, Jiang, Wei, Wang, Wang, Liu, Liu, Chen, Li and Wang.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                Date received : 08 February 2018
                Date accepted : 06 July 2018
                Page count
                Figures: 7, Tables: 2, Equations: 0, References: 91, Pages: 14, Words: 9529
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 41601098
                Funded by: National Key R&D Program of China
                Award ID: 2016YFC0500203
                Award ID: 2016JQ3022
                Funded by: Natural Science Foundation of Shanxi Province 10.13039/501100004480
                Categories
                Subject: Microbiology
                Subject: Original Research

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: bacterial community structure,bacterial diversity,bacterial function,temperate deciduous broad-leaved forest,tropical rainforest,environmental factors
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: bacterial community structure, bacterial diversity, bacterial function, temperate deciduous broad-leaved forest, tropical rainforest, environmental factors

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