Potential Oxygen Consumption and Community Composition of Sediment Bacteria in a Seasonally Hypoxic Enclosed Bay

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.

Download Full-text

Potential oxygen consumption and community composition of sediment bacteria in a seasonally hypoxic enclosed bay

PeerJ ◽

10.7717/peerj.11836 ◽

2021 ◽

Vol 9 ◽

pp. e11836

Author(s):

Fumiaki Mori ◽

Yu Umezawa ◽

Ryuji Kondo ◽

Gregory N. Nishihara ◽

Minoru Wada

Keyword(s):

Oxygen Consumption ◽

16S Rrna Genes ◽

Rrna Genes ◽

Sediment Surface ◽

Tetrazolium Chloride ◽

Sediment Samples ◽

Relative Contribution ◽

Before And After ◽

Seasonal Hypoxia ◽

Potential Oxygen

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 sharp increase in the relative abundance of sulfate reducing bacteria toward hypoxia. In addition, a notable shift in other bacterial compositions was observed before and after the INT assay incubation. It was Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, that increased markedly during the assay period in the summer samples. These findings have implications not only for members of Delta- and Gammaproteobacteria 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.

Download Full-text

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.

Download Full-text

The Bacterial Community Composition of the Bovine Rumen Detected Using Pyrosequencing of 16S rRNA Genes

Metagenomics ◽

10.4303/mg/235571 ◽

2012 ◽

Vol 1 ◽

pp. 1-11 ◽

Cited By ~ 47

Author(s):

Sitao Wu ◽

Ransom L. Baldwin ◽

Weizhong Li ◽

Congjun Li ◽

Erin E. Connor ◽

...

Keyword(s):

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bovine Rumen

Download Full-text

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.

Download Full-text

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.

Download Full-text

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

PLoS ONE ◽

10.1371/annotation/111eaadc-5af4-4d5e-8ae0-7abaebbb6ad6 ◽

2013 ◽

Vol 8 (11) ◽

Author(s):

Daochen Zhu ◽

Shoko-Hosoi Tanabe ◽

Chong Yang ◽

Weimin Zhang ◽

Jianzhong Sun

Keyword(s):

South China Sea ◽

Bacterial Community ◽

16S Rrna ◽

Community Composition ◽

South China ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

China Sea

Download Full-text

Diversity and Metabolism of Marine Bacteria Cultivated on Dissolved DNA

Applied and Environmental Microbiology ◽

10.1128/aem.02674-06 ◽

2007 ◽

Vol 73 (9) ◽

pp. 2799-2805 ◽

Cited By ~ 35

Author(s):

Jay T. Lennon

Keyword(s):

Molecular Weight ◽

Bacterial Community ◽

Community Composition ◽

Marine Bacteria ◽

Bacterial Community Composition ◽

Primary Source ◽

16S Rrna Genes ◽

Rrna Genes ◽

Taxon Richness ◽

Nitrogen And Phosphorus

ABSTRACT Dissolved DNA (dDNA) is a potentially important source of energy and nutrients in aquatic ecosystems. However, little is known about the identity, metabolism, and interactions of the microorganisms capable of consuming dDNA. Bacteria from Eel Pond (Woods Hole, MA) were cultivated on low-molecular-weight (LMW) or high-molecular-weight (HMW) dDNA, which served as the primary source of carbon, nitrogen, and phosphorus. Cloning and sequencing of 16S rRNA genes revealed that distinct bacterial assemblages with comparable levels of taxon richness developed on LMW and HMW dDNA. Since the LMW and HMW dDNA used in this study were stoichiometrically identical, the results confirm that the size alone of dissolved organic matter can influence bacterial community composition. Variation in the growth and metabolism of isolates provided insight into mechanisms that may have generated differences in bacterial community composition. For example, bacteria from LMW dDNA enrichments generally grew better on LMW dDNA than on HMW dDNA. In contrast, bacteria isolated from HMW dDNA enrichments were more effective at degrading HMW dDNA than bacteria isolated from LMW dDNA enrichments. Thus, marine bacteria may experience a trade-off between their ability to compete for LMW dDNA and their ability to access HMW dDNA via extracellular nuclease production. Together, the results of this study suggest that dDNA turnover in marine ecosystems may involve a succession of microbial assemblages with specialized ecological strategies.

Download Full-text

High contribution ofPelagibacteralesto bacterial community composition and activity in spring blooms off Kerguelen Island (Southern Ocean)

10.1101/633925 ◽

2019 ◽

Author(s):

J. Dinasquet ◽

M. Landa ◽

I. Obernosterer

Keyword(s):

Bacterial Community ◽

Southern Ocean ◽

Community Composition ◽

Bacterial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Leucine Incorporation ◽

Tropical Ocean ◽

Kerguelen Island ◽

Sar11 Clade

AbstractThe ecology of Pelagibacterales (SAR11 clade), the most abundant bacterial group in the ocean, has been intensively studied in temperate and tropical ocean regions, but the distribution patterns of this clade remains largely unexplored in the Southern Ocean. Through amplicon sequencing of the 16S rRNA genes, we assessed the contribution of Pelagibacterales to bacterial community composition in the naturally iron fertilized region off Kerguelen Island (Southern Ocean). We investigated the upper 300 m water column at seven sites located in early spring phytoplankton blooms and at one site in HNLC waters. Despite pronounced vertical patterns of the bacterioplankton assemblages, the SAR11 clade had high relative abundances at all depths and sites, averaging 40% (±15%) of the total community relative abundance. Micro-autoradiography combined with CARD-FISH further revealed that the SAR11 clade contributed substantially (45-60% in surface waters) to bacterial biomass production (as determined by3H leucine incorporation). A clear niche partitioning of the further resolved SAR11 subclades was observed with depth layers, but differences among sites were detectable for only a few subclades. Our study provides novel observations of the distribution and contribution to the marine carbon cycle of the SAR11 clade in the cold waters of the Southern Ocean.

Download Full-text