Relative Abundance of Ammonia Oxidizers, Denitrifiers, and Anammox Bacteria in Sediments of Hyper‐<scp>N</scp>utrified Estuarine Tidal Flats and in Relation to Environmental Conditions

Zhang, Xiaoli; Agogué, Hélène; Dupuy, Christine; Gong, Jun

doi:10.1002/clen.201300013

Cited by 20 publications

(19 citation statements)

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“…The total organic carbon (TOC) and total organic nitrogen (TON) contents in the sediments were measured with a Vario Micro Cube elemental analyzer (Elementar, Germany). To determine the concentrations of metals, the sediments were pretreated with 1 M HCl, and the concentrations were then determined with an ELAN DRC II plasma mass spectrometer (an inductively coupled plasma mass spectrometer; PerkinElmer, Hong Kong) (22).…”

Section: Methodsmentioning

confidence: 99%

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Sun

Zhang

et al. 2015

Appl Environ Microbiol

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dSeagrass colonization changes the chemistry and biogeochemical cycles mediated by microbes in coastal sediments. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina-colonized coastal lagoon in northern China. Higher nitrogenase gene (nifH) copy numbers were detected in the sediments from the vegetated region than in the sediments from the unvegetated region nearby. The nifH phylotypes detected were mostly affiliated with the Geobacteraceae, Desulfobulbus, Desulfocapsa, and Pseudomonas. Redundancy analysis based on terminal restriction fragment length polymorphism analysis showed that the distribution of nifH genotypes was mostly shaped by the ratio of total organic carbon to total organic nitrogen, the concentration of cadmium in the sediments, and the pH of the overlying water. High-throughput sequencing and phylogenetic analyses of bacterial 16S rRNA genes also indicated the presence of Geobacteraceae and Desulfobulbaceae phylotypes in these samples. A comparison of these results with those of previous studies suggests the prevalence and predominance of iron(III)-reducing Geobacteraceae and sulfate-reducing Desulfobulbaceae diazotrophs in coastal sedimentary environments. Although the entire bacterial community structure was not significantly different between these two niches, Desulfococcus (Deltaproteobacteria) and Anaerolineae (Chloroflexi) presented with much higher proportions in the vegetated sediments, and Flavobacteriaceae (Bacteroidetes) occurred more frequently in the bare sediments. These data suggest that the high bioavailability of organic matter (indicated by relatively lower carbon-to-nitrogen ratios) and the less-reducing anaerobic condition in vegetated sediments may favor Desulfococcus and Anaerolineae lineages, which are potentially important populations in benthic carbon and sulfur cycling in the highly productive seagrass ecosystem. Sediments colonized by seagrass in shallow estuarine and coastal environments are hot spots of microbial activities. Seagrass meadows enrich the sediment carbon matter by exuding dissolved organic carbon (DOC) through their roots and trapping organic particles from the overlying water (1). Due to the effects of seagrass on nutrient deposition, retention, and mineralization from organic matter, the nutrients in pore water are often richer in seagrass sediments than in sediments from unvegetated regions (1-3). Seagrass roots also release photosynthesis-produced O 2 into sediments, which results in less-reducing conditions in seagrass meadows than unvegetated sediments and contributes to the prevention of the accumulation of sulfides, the toxic products of sulfate reduction in anaerobic sedimentary environments that could play a role in dieback events in seagrass meadows (1, 4). Higher bacterial populations and activities (particularly bacterium-mediated sulfate reduction) are usually found in seagrass-vegetated sites and not in unvegetated sediments (5-8).Because the gro...

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Section: Methodsmentioning

confidence: 99%

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Sun

Zhang

et al. 2015

Appl Environ Microbiol

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“…The physical conditions of three hypernutrified estuarine tidal flats in the mouths of the Jiaolai River (JL), Bailang River (BL) and Di River (Di) of the Laizhou Bay have been described previously in detail (Zhang et al 2014). These three rivers have different pollution histories and discharge sources (e.g.…”

Section: Sampling and Environmental Parameters Analysismentioning

confidence: 99%

“…dying industries, mariculture and brine industries). The sampling and analysis of the environmental parameters, including dissolved oxygen (DO), pH, salinity, and temperature of overlying water, and nitrate, nitrite, ammonium, total organic carbon and nitrogen contents, sediment grain size, and trace metal As, Co, Cd, Cr, Cu, Ni, Pb, Zn levels of sediments, were also performed as described in a previous publication (Zhang et al 2014).…”

Section: Sampling and Environmental Parameters Analysismentioning

confidence: 99%

“…aquaculture, subsurface brine industries and dyeing industries) and agriculture (Hu et al 2010;Zhang et al 2014). These tidal flats thus present ideal environments for studying the multiple environmental stresses on nitrogen-removal microorganisms.…”

Section: Introductionmentioning

confidence: 99%

“…These tidal flats thus present ideal environments for studying the multiple environmental stresses on nitrogen-removal microorganisms. We have carried out an ecological study on benthic microbial nitrogen cycling in this area, and demonstrated that abundances of N-cycling functional groups respond differently to variations of environmental conditions, and the metals Cu and Cd affect AOA/AOB dominance (Zhang et al 2014). As another contribution, this study focused on the following objectives: (1) to investigate the relative importance of spatial (locations, layers) and seasonal controls on the distribution of ammonia oxidizers, denitrifiers, and anammox bacteria; and (2) to test the hypothesis that metals impact the diversity and community composition of the nitrogen microbial community in the estuarine system.…”

Section: Introductionmentioning

confidence: 99%

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Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats

et al. 2014

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The spatial and temporal patterns of diversity, community structure, and their drivers are fundamental issues in microbial ecology. This study aimed to investigate the relative importance of spatial and seasonal controls on the distribution of nitrogen cycling microbes in sediments of estuarine tidal flats, and to test the hypothesis that metals impact the distribution of nitrogen-cycling microbes in the coastal system. Two layers of sediment samples were collected from three estuarine tidal flats of Laizhou Bay in 2010 winter and 2011 summer. The alpha diversities (Shannon and Simpson indices) and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA), denitrifier and anammox bacteria (AMB) were revealed using denaturing gradient gel electrophoresis and clone library analysis of amoA, nosZ and 16S rRNA gene markers. We found that both AOB and AMB exhibited distinct seasonal patterns in either alpha diversity or community turnover; AOA had different alpha diversities in two layers, but neither spatial nor seasonal patterns were found for their community turnover. However, no distinct spatiotemporal pattern was observed for either diversity or community composition of nosZ-type denitrifiers. For correlations between alpha diversities and environmental factors, significant correlations were found between AOB and ammonium, temperature and As, between denitrifiers and nitrite, salinity and Pb, and between AMB and Pb, ratio of organic carbon to nitrogen, ammonium, pH and dissolved oxygen. Salinity and sediment grain size were the most important factors shaping AOB and AOA communities, respectively; whereas AMB community structure was mostly determined by temperature, dissolved oxygen, pH and heavy metals As and Cd. These results stress that ammonia oxidizers, denitrifiers and anammox bacteria have generally different distributional patterns across time and space, and heavy metals might have contributed to their differentiated distributions in coastal sediments.

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The Microbiome of Coastal Sediments

Underwood

Dumbrell

McGenity

et al. 2022

The Microbiomes of Humans, Animals, Plants, and the Environment

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Coastal zones are amongst the most productive marine environments and many are highly impacted by anthropogenic activity. Coastal zones are key regions for the transformation of land-based inputs of nutrients and pollutants and provide many essential ecosystem services for human society. Periods of tidal exposure and submergence, coupled with seasonal variation in land-based inputs, result in intertidal habitats characterized by highly variable environmental conditions that pose crucial adaptive challenges for organisms. This review focusses on the microbiome of coastal sediments consisting of protists (especially diatoms), bacteria, archaea and fungi. The diversity, distribution, production, adaptations, and interactions between these groups are reviewed. Coastal microbiomes are characterized by high rates of biogeochemical activity. Photoautotrophic diatoms exhibit complex patterns of behavior to cope with a highly variable light climate. Multiple species-species interactions between autotrophs and heterotrophs contribute to the cycling of carbon and nitrogen. In sediments, autotrophic and heterotrophic processes are closely coupled both spatially and temporally. Bacteria and archaea control the nitrogen-and carbon cycles while taxonomic diversity is influenced by gradients of organic matter, nitrogen compounds, sulfide, and oxygen. Fungi are important components of coastal salt marsh sediment microbiomes but their role in unvegetated sediments is less well understood. This review considers the high human impact on coastal sediments and the importance of nutrient gradients and pollution pressures (hydrocarbons) in affecting diversity and species distribution.

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Relative Abundance of Ammonia Oxidizers, Denitrifiers, and Anammox Bacteria in Sediments of Hyper‐Nutrified Estuarine Tidal Flats and in Relation to Environmental Conditions

Cited by 20 publications

References 58 publications

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Seagrass (Zostera marina) Colonization Promotes the Accumulation of Diazotrophic Bacteria and Alters the Relative Abundances of Specific Bacterial Lineages Involved in Benthic Carbon and Sulfur Cycling

Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats

The Microbiome of Coastal Sediments

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