Correction: Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Abstract The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a notable shift in the bacterial community composition before and after the INT assay incubation. Within the bacterial community that was predominated by the ASVs closely related to Woeseia (Woeseiaceae, Gammaproteobacteria), the relative abundance of ASVs affiliated with Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, increased markedly in the summer samples. These findings have implications not only for the group of bacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

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Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

International Journal of Molecular Sciences ◽

10.3390/ijms20112619 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2619 ◽

Cited By ~ 7

Author(s):

Ahmad Ali ◽

Muhammad Imran Ghani ◽

Yuhong Li ◽

Haiyan Ding ◽

Huanwen Meng ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Chinese Cabbage ◽

Cropping Systems ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Crop Diversification ◽

Soil Microbial ◽

Heading Chinese Cabbage

Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach–cucumber (SC) and non-heading Chinese cabbage–cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce–cucumber (LLC), coriander–cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host–plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non–heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop–soil sustainable intensification.

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Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

10.5194/bg-2019-214 ◽

2019 ◽

Author(s):

Edwin Sien Aun Sia ◽

Zhuoyi Zhu ◽

Jing Zhang ◽

Wee Cheah ◽

Jiang Shan ◽

...

Keyword(s):

South China Sea ◽

Microbial Communities ◽

Community Composition ◽

South China ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Drainage System ◽

Rrna Gene ◽

China Sea ◽

Biogeographical Distribution

Abstract. Microbial community composition and diversity in freshwater habitats, especially in lotic environments, are much less studied compared to marine and soil communities. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes whereby peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River-South China Sea continuum. This was carried out utilizing 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 μm GF/C filter membranes) covering different biogeographical features/sources from headwaters to coastal waters. The microbial communities found along the Rajang river exhibited taxa common to rivers (i.e. the predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α- and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along the salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the Rajang River to sea continuum, the PICRUST predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem health in response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

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Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial community composition in deep-sea sediments of the South China Sea

World Journal of Microbiology and Biotechnology ◽

10.1007/s11274-006-9181-x ◽

2006 ◽

Vol 22 (12) ◽

pp. 1337-1345 ◽

Cited By ~ 18

Author(s):

Xintian Lai ◽

Xiaofan Zeng ◽

Shu Fang ◽

Yali Huang ◽

Lixiang Cao ◽

...

Keyword(s):

South China Sea ◽

Bacterial Community ◽

Community Composition ◽

South China ◽

Deep Sea ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Community Composition ◽

The South China Sea ◽

Gradient Gel Electrophoresis

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Effect of Elevated Tropospheric Ozone on the Structure of Bacterial Communities Inhabiting the Rhizosphere of Herbaceous Plants Native to Germany

Applied and Environmental Microbiology ◽

10.1128/aem.71.12.7750-7758.2005 ◽

2005 ◽

Vol 71 (12) ◽

pp. 7750-7758 ◽

Cited By ~ 46

Author(s):

Anja B. Dohrmann ◽

Christoph C. Tebbe

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Poa Pratensis ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Herbaceous Plants ◽

Rrna Genes ◽

Detectable Effect ◽

Rrna Gene ◽

Gene Probe

ABSTRACT Current elevated concentrations of ozone in the atmosphere, as they are observed during summer seasons, can cause severe effects on plant vegetation. This study was initiated to analyze whether ozone-stressed plants also transfer signals below ground and thereby alter the bacterial community composition in their rhizospheres. Herbaceous plants, native to Germany, with tolerance (Anthoxanthum odoratum, Achillea millefolium, Poa pratensis, Rumex acetosa, and Veronica chamaedrys) and sensitivity (Matricaria chamomilla, Sonchus asper, and Tanacetum vulgare) to ozone, raised in the greenhouse, were exposed in open-top chambers to two different ozone regimes, i.e., “summer stress” and a normal ozone background. DNA of bacterial cells from the rhizospheres was directly extracted, and partial sequences of the 16S rRNA genes were PCR amplified with primers targeting the following phylogenetic groups: Bacteria, α-Proteobacteria, Actinobacteria, and Pseudomonas, respectively. The diversity of the amplified products was analyzed by genetic profiling based on single-strand conformation polymorphism (SSCP). Neither the tolerant nor the sensitive plants, the latter with visible above-ground damage, showed ozone-induced differences in any of the SSCP profiles, with the single exception of Actinobacteria-targeted profiles from S. asper. To increase the stress, S. asper was germinated and raised in the continuous presence of an elevated level of ozone. SSCP profiles with Bacteria-specific primers combined with gene probe hybridizations indicated an ozone-related increase in a Xanthomonas-related 16S rRNA gene and a decrease in the respective gene from the plant plastids. The fact that only this latter unrealistic scenario caused a detectable effect demonstrated that ozone stress has a surprisingly small effect on the structural diversity of the bacterial community in rhizospheres.

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Respiratory Succession and Community Succession of Bacterioplankton in Seasonally Anoxic Estuarine Waters

Applied and Environmental Microbiology ◽

10.1128/aem.00648-07 ◽

2007 ◽

Vol 73 (21) ◽

pp. 6802-6810 ◽

Cited By ~ 61

Author(s):

Byron C. Crump ◽

Cherie Peranteau ◽

Barbara Beckingham ◽

Jeffrey C. Cornwell

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Nitrate Respiration ◽

Leucine Incorporation ◽

Anoxic Water ◽

Anoxic Waters

ABSTRACT Anoxia occurs in bottom waters of stratified estuaries when respiratory consumption of oxygen, primarily by bacteria, outpaces atmospheric and photosynthetic reoxygenation. Once water becomes anoxic, bacterioplankton must change their metabolism to some form of anaerobic respiration. Analysis of redox chemistry in water samples spanning the oxycline of Chesapeake Bay during the summer of 2004 suggested that there was a succession of respiratory metabolism following the loss of oxygen. Bacterial community doubling time, calculated from bacterial abundance (direct counts) and production (anaerobic leucine incorporation), ranged from 0.36 to 0.75 day and was always much shorter than estimates of the time that the bottom water was anoxic (18 to 44 days), indicating that there was adequate time for bacterial community composition to shift in response to changing redox conditions. However, community composition (as determined by PCR-denaturing gradient gel electrophoresis analysis of 16S rRNA genes) in anoxic waters was very similar to that in surface waters in June when nitrate respiration was apparent in the water column and only partially shifted away from the composition of the surface community after nitrate was depleted. Anoxic water communities did not change dramatically until August, when sulfate respiration appeared to dominate. Surface water populations that remained dominant in anoxic waters were Synechococcus sp., Gammaproteobacteria in the SAR86 clade, and Alphaproteobacteria relatives of Pelagibacter ubique, including a putative estuarine-specific Pelagibacter cluster. Populations that developed in anoxic water were most similar (<92% similarity) to uncultivated Firmicutes, uncultivated Bacteroidetes, Gammaproteobacteria in the genus Thioalcalovibrio, and the uncultivated SAR406 cluster. These results indicate that typical estuarine bacterioplankton switch to anaerobic metabolism under anoxic conditions but are ultimately replaced by different organisms under sulfidic conditions.

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Permeable Reactive Barriers Designed To Mitigate Eutrophication Alter Bacterial Community Composition and Aquifer Redox Conditions

Applied and Environmental Microbiology ◽

10.1128/aem.01986-15 ◽

2015 ◽

Vol 81 (20) ◽

pp. 7114-7124 ◽

Cited By ~ 9

Author(s):

Kenly A. Hiller ◽

Kenneth H. Foreman ◽

David Weisman ◽

Jennifer L. Bowen

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

16S Rrna ◽

Bacterial Community Composition ◽

Environmental Parameters ◽

Permeable Reactive Barriers ◽

16S Rrna Genes ◽

Rrna Genes ◽

Reactive Barriers

ABSTRACTPermeable reactive barriers (PRBs) consist of a labile carbon source that is positioned to intercept nitrate-laden groundwater to prevent eutrophication. Decomposition of carbon in the PRB drives groundwater anoxic, fostering microbial denitrification. Such PRBs are an ideal habitat to examine microbial community structure under high-nitrate, carbon-replete conditions in coastal aquifers. We examined a PRB installed at the Waquoit Bay National Estuarine Research Reserve in Falmouth, MA. Groundwater within and below the PRB was depleted in oxygen compared to groundwater at sites upgradient and at adjacent reference sites. Nitrate concentrations declined from a high of 25 μM upgradient and adjacent to the barrier to <0.1 μM within the PRB. We analyzed the total and active bacterial communities filtered from groundwater flowing through the PRB using amplicons of 16S rRNA and of the 16S rRNA genes. Analysis of the 16S rRNA genes collected from the PRB showed that the total bacterial community had high relative abundances of bacteria thought to have alternative metabolisms, such as fermentation, including candidate phyla OD1, OP3, TM7, and GN02. In contrast, the active bacteria had lower abundances of many of these bacteria, suggesting that the bacterial taxa that differentiate the PRB groundwater community were not actively growing. Among the environmental variables analyzed, dissolved oxygen concentration explained the largest proportion of total community structure. There was, however, no significant correlation between measured environmental parameters and the active microbial community, suggesting that controls on the active portion may differ from the community as a whole.

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Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6784-6792.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6784-6792 ◽

Cited By ~ 114

Author(s):

Naoise Nunan ◽

Timothy J. Daniell ◽

Brajesh K. Singh ◽

Artemis Papert ◽

James W. McNicol ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Bacterial Community Composition ◽

Molecular Techniques ◽

16S Rrna Genes ◽

Rrna Genes ◽

Grassland Soils

ABSTRACT Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

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