Bacteria In Coastal Sediments Research Articles

Fungal-bacterial network in PAH-contaminated coastal marine sediment.

Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.

A Simple Culture Method Enhances the Recovery of Culturable Actinobacteria From Coastal Sediments.

Molecular methods revealed that the majority of microbes in natural environments remains uncultivated. To fully understand the physiological and metabolic characteristics of microbes, however, culturing is still critical for microbial studies. Here, we used bacterial community analysis and four culture media, namely, traditional marine broth 2216 (MB), water extracted matter (WEM), methanol extracted matter (MEM), and starch casein agar (SCA), to investigate the diversity of cultivated bacteria in coastal sediments. A total of 1,036 isolates were obtained in pure culture, and they were classified into five groups, namely, Alphaproteobacteria (52.51%), Gammaproteobacteria (23.26%), Actinobacteria (13.32%), Firmicutes, and Bacteroidetes. Compared to other three media, WEM recovered a high diversity of actinobacteria (42 of 63 genotypes), with Micromonospora and Streptomyces as the most cultivated genera. Amplicon sequencing of the bacterial 16S ribosomal RNA (rRNA) gene V3–V4 fragment revealed eight dominant groups, Alphaproteobacteria (12.81%), Gammaproteobacteria (20.07%), Deltaproteobacteria (12.95%), Chloroflexi (13.09%), Bacteroidetes (8.28%), Actinobacteria (7.34%), Cyanobacteria (6.20%), and Acidobacteria (5.71%). The dominant members affiliated to Actinobacteria belonged to “Candidatus Actinomarinales,” “Candidatus Microtrichales,” and Nitriliruptorales. The cultivated actinobacteria accounted for a small proportion (<5%) compared to the actinobacterial community, which supported that the majority of actinobacteria are still waiting for cultivation. Our study concluded that WEM could be a useful and simple culture medium that enhanced the recovery of culturable actinobacteria from coastal sediments.

Identification of Aerobic Methane-Oxidizing Bacteria in Coastal Sediments of the Crimean Peninsula

Methane oxidation rates and diversity of methane-oxidizing microorganisms in the upper sediment layers of the Crimean Peninsula coastal regions (Black Sea) were investigated. Analysis of the 16S rRNA gene sequences revealed microorganisms of the class Gammaproteobacteria, order Methylococcales. At the sites of continuous gas seepage, the percentage of methanotrophs in the bacterial community was high (up to 2.1% of the total read number), which made it possible to detect them by sequencing of the native samples. At the sites of intermittent gas seepage formed during summer and autumn, methanotrophs were minor components of the communities and could be detected only after incubation of the sediment samples in the presence of methane. Low similarity between their 16S rRNA sequences and those of the known methanotrophs indicates that some organisms probably belong to new taxa of the species and genus levels.

Anaerobnyye bakterii v pribrezhnykh nanosakh bukhty Troitskoy (Sevastopol', Chernoye more)

Anaerobnyye bakterii v pribrezhnykh nanosakh bukhty Troitskoy (Sevastopol', Chernoye more)

Spatial Abundance, Diversity, and Activity of Ammonia-Oxidizing Bacteria in Coastal Sediments of the Liaohe Estuary

Ammonia-oxidizing bacteria (AOB) play an important role in nitrification in estuaries. The aim of this study was to examine the spatial abundance, diversity, and activity of AOB in coastal sediments of the Liaohe Estuary using quantitative PCR, high-throughput sequencing of the amoA gene coding the ammonia monooxygenase enzyme active subunit, and sediment slurry incubation experiments. AOB abundance ranged from 8.54 × 104 to 5.85 × 106 copies g-1 of wet sediment weight and exhibited an increasing trend from the Liaohe Estuary to the open coastal zone. Potential nitrification rates (PNRs) ranged from 0.1 to 336.8nmol N g-1 day-1 along the estuary to the coastal zone. Log AOB abundance and PNRs were significantly positively correlated. AOB richness decreased from the estuary to the coastal zone. High-throughput sequencing analysis indicated that the majority of amoA gene sequences fell within the Nitrosomonas and Nitrosomonas-like clade, and only a few sequences were clustered within the Nitrosospira clade. This finding indicates that the Nitrosomonas-related lineage may be more adaptable to the specific conditions in this estuary than the Nitrosospira lineage. Sites with high nitrification rates were located in the southern open region and were dominated by the Nitrosomonas-like lineage, whereas the Nitrosospira lineage was found primarily in the northern estuary mouth sites with low nitrification rates. Thus, nitrification potentials in Liaohe estuarine sediments in the southern open region were greater than those in the northern estuary mouth, and the Nitrosomonas-related lineage might play a more important role than the Nitrosospira lineage in nitrification in this estuary.

Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

Influence of Freshwater Sediment Characteristics on Persistence of Fecal Indicator Bacteria

Extended persistence of enteric bacteria in coastal sediments and potential remobilization of pathogens during natural turbulence or human activities may induce an increased risk of human infections. In this study, the effect of sediment characteristics such as particle grain size and nutrient and organic matter contents on the survival of fecal indicator bacteria (FIB) including total coliforms, Escherichia coli, and Enterococcus was investigated. The experimentation was carried out for 50 days in microcosms containing lake water and different contaminated freshwater sediments in continuous-flow and batch conditions. Results of this study revealed: (1) extended FIB survival in sediments up to 50 days, (2) higher growth and lower decay rates of FIB in sediments with high levels of organic matter and nutrients and small (mainly silt) grain size, and (3) longer survival of Enterococcus sp. compared to E. coli and total coliforms. FIB survival in sediments and possible resuspension are of considerable significance for the understanding of permanent microbial pollution in water column and therefore human risk during recreational activities.

Environmental controls on the speciation and distribution of mercury in coastal sediments

Methylmercury production by sulfate reducing bacteria in coastal sediments leads to bioaccumulation of mercury in fish, shellfish, and ultimately humans. Sulfur, organic carbon, and sediment structure and composition can all affect methylmercury production by changing the amount of bioavailable inorganic mercury and by stimulating the activity of methylating microbes. This study investigates total and methylmercury in solids and porewaters relative to total sulfide concentration, redox potential, sediment grain size, and total organic carbon in a range of sediment types from the Bay of Fundy region of Canada. Using these data, we construct a conceptual model of the biogeochemical environment surrounding methylating microbes in high sulfide, organically enriched sediments. Whereas other studies of methylmercury dynamics measured porewater sulfide concentrations in relatively low-sulfide systems (∼20–300 μM), we measured total sulfide levels using a method developed to indicate organic enrichment across a much wider range of sulfidic sediments (10–4000 μM). We observed that higher sulfide concentrations correspond to an elevated fraction of mercury in methylated form suggesting higher net methylation rates in these sediments. This relationship is strongest in sediments that are moderately impacted by organic enrichment, but weak in less impacted, aerobic sediments. Higher sulfide concentrations in porewaters containing dissolved organic matter appear to yield a geochemical environment that is conducive to uptake of Hg(II) by methylating bacteria. Data collected in this study imply that moderate levels of organic enrichment through fish farming may enhance methylmercury production in the Bay of Fundy.

Interrelationships between sulfate reducing and methane producing bacteria in coastal sediments with intense sulfide production

Coastal sediments receiving different amounts of organic carbon through sedimentation were investigated with respect to sulfate reduction and methanogenic activity. Sampling was carried out at sediment temperatures of 7° and 15°C. Sulfate-reducing and methanogenic bacteria were found at all depths. Sulfate reduction decreased with depth and the highest sulfide concentrations were found a few centimeters below the sediment surface, up to 15 mM at 15°C and pH 7.1. In the same segments a maximum in the methane concentration was also found, 0.91 mM. The high sulfide concentration inhibited the methane formation from acetate but not from carbon dioxide. In the organic rich sediment sulfate reduction was limited by the diffusion of SO 4 + into the sediment and methane production from acetate by sulfide diffusion out of the sediment. When electron acceptor concentration limits sulfate reduction, thermodynamic calculations show that the utilization of electron donors more reduced than acetate is favored. In the sediment with the high carbon-input, acetate predominated at 15°C whereas in the low carbon-input sediment hardly any short chain organic acids were detected. The possibility of a shift in sulfate reduction from acetate oxidation to acetate production is discussed.

Simultaneous determinations of nitrification and nitrate reduction in coastal sediments by a 15N dilution technique.

Nitrification, the oxidation of ammonia to nitrite and nitrate, and nitrate reduction by bacteria in coastal sediments of Mangoku-Ura and Odawa Bay were simultaneously determined by a 15N dilution technique. In muddy sediments of Mangoku-Ura, nitrate reduction proceeded at a rate of 10(-2) to 10 X 10(-2) microgram-atoms of N/g per h. Nitrification was far less intensive. Denitrification, or N2 production from nitrate, accounted for about 30% of the nitrate reduction. A simultaneous occurrence of nitrification and nitrate reduction with a similar rate of 10(-2) microgram-atoms of N/g per h was demonstrated in sandy sediment collected from a Zostera bed of Odawa Bay.