Microbial Diversity In Sediments Research Articles

Study on water quality safety and microbial diversity of water source reservoirs in Daqing City

Water source reservoirs play a vital role in ensuring the drinking water safety. To explore the safety of water quality as the source of water supply projects in Daqing City, the chemical indexes of water quality in Daqing reservoir, Dongcheng reservoir and Hongqi reservoir were analyzed. The microbial diversity, community structure characteristics and Nitrogen metabolism functional bacteria were analyzed by high-throughput sequencing technology. Monitor the disinfection effect of three water source reservoirs after using sodium hypochlor disinfection. The results showed that, in 2021, the reservoirs water body was in a moderately eutrophic state, the main exceeding standard index was total nitrogen (TN) (1.25–1.57 mg/L). The microbial communities in water body and sediments were composed of 1048 genera. The microbial diversity in sediment was higher than that in water. Potential pathogenic microorganisms were detected in water and sediment samples. Although no coliform bacteria were detected, as a water source disinfection was also necessary. Redundancy analysis (RDA) showed that, the main water quality factors affecting microbial community structure in water samples were pH, in sediment samples were water temperature (WT), dissolved oxygen (DO), TN and total phosphorus (TP). Sodium hypochlorite has a good disinfection effect and can ensure the safety of drinking water.

Response of the microbial community structure to the environmental factors during the extreme flood season in Poyang Lake, the largest freshwater lake in China.

Poyang Lake is the largest freshwater lake in China, and there are several studies on the composition and diversity of bacteria in Poyang Lake, while few quantitative studies were carried out on the response of the bacterial community to environmental factors during the extreme flood season in Poyang Lake. The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020. Illumina high-throughput sequencing technology was used in this study. The bacterial community structure in the water was different from that in the sediment of Poyang Lake during extreme flood seasons. The bacterial diversity in water was much lower than that in sediment. In the water column, the dominant phyla were Actinobacteriota, while the composition of bacteria in sediment was more complex than that in water, and the dominant phyla in sediment were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteriota. The bacterial diversity in the water of Poyang Lake showed seasonal dynamics, while no seasonal variation of bacterial communities in sediment was observed. The bacterial community structure in the sediment from the two bays and channel areas of Poyang Lake can be distinguished from each other. The microbial diversity in sediment gradually increased from the Sancha Bay to the Zhouxi Bay and then to the channel, but the total nitrogen (TN) concentration in sediment (STN) and the total phosphorus (TP) concentration in sediment (STP) showed opposite trends. This might be due to the anthropogenic disturbances from the extreme flood. The bacterial community structure in, water column was significantly correlated with WT, NH4-N, STP, SOM, Chl a, DO, TP, and Eh, while the bacterial community structure in sediment was significantly correlated with SOM and STP. The bacterial community structure in water was greatly different from that in sediment in Poyang Lake during extreme flood seasons. The bacterial community structure in the water column was not only sensitive to the geochemical characteristics of the water but also affected by some nutrient concentrations in the sediment. During the wet seasons, bacterial diversity was only affected by SOM and STP.

Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou—The largest artificial lake in southwest China

This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.

Effects of Nutrient Levels on Microbial Diversity in Sediments of a Eutrophic Shallow Lake

Microorganisms can both indicate the water quality characteristics and the health of the aquatic environment, which have an important influence on the cycling of organic carbon, nitrogen (N), and phosphorus (P) in nature. In this study, we took Taihu Lake, a typical eutrophic lake in China, as the research object, and monitored the northern (Changzhou City) and southern (Changxing County) regions of Taihu Lake for three consecutive years (2019–2021), respectively. We also analyzed the microbial diversity in sediments, and then summarized the effects of different nutrient environments on microorganisms in the aquatic environment. The results showed that the pollution level in the northern part of Taihu Lake was higher than that in the southern region of Taihu Lake, where the pollution was mainly in summer (June–July). The pollution in the southern region of Taihu Lake is relatively stable between 2019 and 2021; the changes in the northern part of Taihu Lake are relatively significant. Microbial diversity in the study area was negatively correlated with the degree of eutrophication of water bodies; microbial abundance was positively correlated with nutrient levels. The functional difference analysis indicated that the microorganisms in the sediments of Taihu Lake in the study area were involved in the nutrient transport and transformation, and played an important role in the purification of the lake water body. This study reveals the relationship between water eutrophication and microbial diversity, and then provides a theoretical basis for the management of eutrophic lakes.

Ecological effects of antibiotics on aquaculture ecosystems based on microbial community in sediments

Antibiotics are commonly used in aquaculture facilities during the production cycle, resulting in the gradual development of antibiotic adaptability with prolonged aquaculture histories. Three concentrations (0 (control), 10 mg/kg, and 1000 mg/kg) of each antibiotic (oxytetracycline (OTC), sulfadiazine (SD))were re-entered and were left with four months exposure in the aquaculture sediments of shrimp ponds with an approximately long-term drug application history (5, 15, and more than 30 years). In sediments with 5 (sediment A) and 30 years aquaculture histories (sediment C), microbial diversity (Chao1 Index and Shannon Index) had no significant change with the increasing SD or OTC concentration. In sediment with 15 years aquaculture history (sediment B), microbial diversity decreased significantly with increasing OTC concentration, but showed a tendency to first decrease and then increase with an increasing SD concentration. Meanwhile, both indices of microbial diversity in sediment A were significantly lower than that in sediment B and C. The dominating phyla in all samples were Proteobacteria, Chloroflexi, Firmicutes, Bacteroidetes, and Planctomycetes, while the top 5 genera included Sulfurovum, Methylophaga, Sulfurimonas, Thioalkalispira, and Desulfobulbus, whose relative abundance varied with aquaculture history and antibiotic concentration. The function profiles of the bacterial community (Kyoto Encyclopedia of Genes and Genomes) showed that three pathways of membrane transport, amino acid metabolism, and carbohydrate metabolism were inhibited in microcosms with antibiotics. These findings illustrated that microbial communities in sediment with 5 years aquaculture histories and 15 years aquaculture histories were more sensitive to antibiotics than the microbial community in sediment with 30 years aquaculture histories. And, microbial community in sediment gradually formed antibiotic resistance/tolerance profiles during the long-term antibiotic application.

典型冷暖季沉水植物凋落物分解特性及沉积物微生物群落变化

PDF HTML阅读 XML下载 导出引用 引用提醒 典型冷暖季沉水植物凋落物分解特性及沉积物微生物群落变化 DOI: 10.5846/stxb202106281715 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家水体污染控制与治理科技重大专项（2018ZX07110003）；国家自然科学基金项目（31670467） Decomposition characteristics of typical warm season and cold season submerged plant litters and change of microbial community in sediment Author: Affiliation: Fund Project: National Major Science and Technology Program-“Water Body Pollution Control and Remediation” (2018ZX07110003), National Natural Science Foundation of China (31670467) 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为研究湿地沉水植物腐败分解对水体的污染状况，选择典型沉水植物金鱼藻（暖季植物）和菹草（冷季植物）进行了为期60 d的凋落物分解实验。结果表明金鱼藻和菹草凋落物分解规律相似，0-15 d快速分解，15-60 d缓慢分解，60 d凋落物失重率分别达到60.43%和66.72%。菹草的有机物释放量明显高于金鱼藻，N和P释放量相反，分解释放的N主要是NH+4-N和有机氮。三维荧光光谱（EEMs）结合平行因子分析法解析出一种类色氨酸物质C2和3种类腐殖质物质C1、C3、C4，易降解的类色氨酸有机物先增加后减少，难降解的类富里酸和类腐殖酸有机物逐渐增加。EEMs和四种组分的最大荧光强度百分比表明，溶解性有机物（DOM）在0-15 d以易降解有机物为主，15-60 d以难降解有机物为主。两种植物凋落物分解释放的DOM含量及特性不同，整体上呈低腐殖化特征，可能是水中难降解DOM的一个重要来源。植物凋落物的分解促进了沉积物中微生物的丰富度，降低了微生物的多样性；参与分解的主要微生物包括4 d时的Pseudomonas属（26%-35%）、15 d和30 d时的Malikia属（>8%）和Bacillus属（2.6%-9%），分解难降解有机物的微生物逐渐增加，如Flavobacterium属；沉积物中微生物群落结构的变化受营养物质可利用性变化的影响。分析发现植物凋落物分解对水质的影响具有阶段性，0-15 d，N和P释放量增加暂时导致了水质恶化；15-60 d，N和P释放量降低，难降解有机物含量逐渐增加，可能会加剧水体甚至是沉积物的腐殖化程度。因此，在植物衰亡期应及时打捞或者做好植物平衡收割管理，避免因植物大量腐败导致水质恶化。 Abstract:In order to study the pollution of submerged plant litter decomposition in wetland, a 60-days litter decomposition experiment was carried out with typical submerged plants, including Ceratophyllum demersum L. (warm season plant) and Potamogeton crispus L. (cold season plant). The results showed that decomposition process of both plant litters was similar, a fast decomposition from 0 to 15 d followed by slow decomposition from 15 to 60 d. The mass loss of plant litters on 60 d reached 60.43% and 66.72%, respectively. More organic matters were obviously released from Potamogeton crispus L. than those from Ceratophyllum demersum L., while nitrogen and phosphorus release was the opposite. The nitrogen released was mainly ammonia nitrogen and organic nitrogen. Excitation emission matrix parallel factor analysis identified four kinds of fluorescence components:tryptophan-like C2, and three kinds of humus-like C1, C3, C4. The easily biodegradable tryptophan-like organic matters increased first and then decreased, while the difficult biodegradable fulvic acid-like and humic acid-like organic matters increased gradually. Three-dimensional fluorescence spectra and the maximum fluorescence intensity percentages of the four components showed that dissolved organic matter (DOM) was dominated by easily degradable organic compounds during 0-15 d and by refractory organic compounds during 15-60 d. The contents and characteristics of DOM released during the decomposition of plant litters were different, showing a low humification feature on the whole, which may be an important endogenous source of difficult biodegradable DOM in water. The decomposition of plant litters improved the microbial richness and decreased the microbial diversity in sediments. The main microorganisms included Pseudomonas (26%-35%) at 4 d, Malikia (>8%) and Bacillus (2.6%-9%) at 15 d and 30 d for decomposition, while the microorganisms that decomposed the refractory organic matter increased gradually, such as Flavobacterium. Changes in microbial community structure in sediments were influenced by changes in the availability of nutrients. The results showed that the effects of plant litter decomposition on water quality were phased. The release nitrogen and phosphorus increased during 0-15 d, which led to the deterioration of water quality temporarily; during 15-60 d, nitrogen and phosphorus release decreased, while refractory organic matter content increased gradually, which may exacerbate the humification degree of water and even sediment. Therefore, in the decay period of plant litters, it is necessary to salvage plant litters in time or manage plant harvesting rationally to avoid the deterioration of water quality caused by plant litter decay. 参考文献 相似文献 引证文献

Risk assessments of emerging contaminants in various waters and changes of microbial diversity in sediments from Yangtze River chemical contiguous zone, Eastern China

Over recent decades, increasing chemical contamination has greatly affected aquatic life and human health, even though most contaminants are present at low concentrations. The large-scale chemical industrial parks (CIPs) concentrated in the Yangtze River Delta account for over half of the total in China, and Jiangsu Province occupies one fifth of the Yangtze River Delta. Inevitably, the ecosystems could be affected by these CIPs. In this study, we collected 35 water and 12 sediment samples from the Yangtze River (Taizhou section) surrounding waters adjacent to concentrated CIPs and determined their cumulative chemical levels to be 0.2 to 28.4 μg/L and cumulative detections to be 11 to 39 contaminants with a median of 20 contaminants. 61 out of 153 screened chemicals were detected from at least one sampling site, and 6 contaminants, mostly semi-volatile organic compounds, appeared at all sites. Among these detected chemicals, di-n-octyl phthalate and dibutyl phthalate were at the highest levels. Ecological assessment revealed that 4-chloroaniline, phenol and dibutyl phthalate possibly would induce adverse effects on Yangtze River (Taizhou) ecosystems. Further aided with an evaluation of integrated biomarker response (IBR) index, it was found that site W06 (downstream of Binjiang CIP wastewater inlet) was the location in greatest need of urgent action. As a result, the microbial diversity of sediments in the Yangtze River mainstream was significantly higher than that of tributaries, where CIPs wastewater entered.

Microbial Diversity Analysis of Sediment from Yeosu New Harbor of South Korea Using 16S rRNA Gene Amplicon Sequencing.

The Yeosu New Harbor in the South Korean benthic environment shows a mesotrophic environment affected by the Tsushima Current and the Seomjin River. Here, we report microbial diversity in sediments of Yeosu New Harbor based on 16S rRNA gene amplicon sequencing. The dominant bacterial phylum was Proteobacteria (relative abundance, 72.5 to 78.1%).

Microbial diversity of sediments from an inactive hydrothermal vent field, Southwest Indian Ridge

The Southwest Indian Ridge, which is the slowest-spreading of the main ridges, separates the African and Antarctic plates. The slow expanding rate is associated with less density of hydrothermal vent fields, shorter longevity of hydrothermal activity, cold mantle temperatures and thick lithosphere. However, the microbial communities adapting to such specific characteristics of this area have remained largely unexplored. To study the microbial diversity at the Southwest Indian Ridge, we sampled three sediment cores in a newly found inactive vent field, the Tianzuo field, and used high-throughput sequencing of 16S rRNA genes to reveal the microbial composition. Microbial communities of three sampling sites were very similar at the surface, and underwent a gradient change along depth. Gammaproteobacteria, namely Alteromonadaceae, Nitrosococcus and the JTB255 marine benthic group, were the most dominant bacterial taxa. Marine Group I was the dominant archaeal taxon in our samples. In addition, microbial populations capable of ammonia oxidation, nitrite oxidation, sulfur oxidation and manganese oxidation were detected to be the main chemolithoautotrophs. The enrichment of sulfur-oxidizing and manganese-oxidizing bacteria was observed in deep layers. When compared with other vent fields along different ocean ridges, the Tianzuo field showed distinct composition in both archaeal and bacterial communities. These results provide the first view of microbial communities of the Tianzuo field at the Southwest Indian Ridge, and give a better understanding of metabolic potential possessed by the microbial populations.

Microbial diversity in the sediments of the southern Mariana Trench

Microbial diversity in the abyssal sediments beneath the seafloor of 30, 94, and 151 cm near the southern end of the Mariana Trench was analyzed in the Illumina HiSeq 2500 platform. Results show that the microbial populations were dominated by bacteria but merely no archaea were identified at the three depths. In the bacterial community, Proteobacteria and Firmicutes dominated the total taxon tags, followed by Bacteroidetes, Actinobacteria, Planctomycetes, Cyanobacteria, and Chloroflexi, which together account for over 99% of the total population. Similar to that in the seawater in the trench, the operational taxonomic units (OTUs) belonging to Gammaproteobacteria from the sediment samples showed high abundance. However, common bacterial OTUs in the water of the trench including Nitrospirae and Marinimicrobia were hardly found in the sediments from the southern Mariana Trench or the hadal region. Therefore, this study documented for the first time the compositions of microbial diversity in the trench sediments, revealed the difference in microbial diversity in water and sediment of the trench and will enrich the knowledge on the microbial diversity in the abyssal areas.

Microbial Diversity Analysis of Sediment from Nakdong River Estuary in the Republic of Korea Using 16S rRNA Gene Amplicon Sequencing.

Deterioration of sediment quality has been found in the Nakdong River Estuary after large-scale reclamations. Here, I report microbial diversity in sediments of Nakdong River Estuary in the Republic of Korea based on 16S rRNA gene sequencing by next-generation sequencing (NGS) techniques. The dominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes, and Planctomycetes.

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench.

The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.

Comparative Study of Guaymas Basin Microbiomes: Cold Seeps vs. Hydrothermal Vents Sediments

In the Guaymas Basin, the presence at a few tens of kilometers of cold seeps and hydrothermal vents coupled with comparable sedimentary settings and depths offer a unique opportunity to assess and compare the microbial community composition of these deep-sea ecosystems. The microbial diversity in sediments from three cold seep and two hydrothermal vent assemblages were investigated using high-throughput 16S rRNA-sequencing. Numerous bacterial and archaeal lineages were detected in both cold seep and hydrothermal vent sediments. Various potential organic matter degraders (e.g. Chloroflexi, Atribacteria, MBG-D) and methane and sulfur cycling related microorganisms (e.g. ANME and methanogenic lineages, sulfate-reducing lineages) were detected in both ecosystems. This suggests that analogous metabolic processes such as organic matter degradation and anaerobic methane oxidation coupled to sulfate reduction, were probably occurring in these two contrasted ecosystems. These highlighted core microbiome of the Guaymas Basin chemosynthetic ecosystems might therefore result from the combined presence of up-rising fluid emissions and high sedimentary rates of organic matter in the Basin. These results, coupled with the detailed ribotype analysis of major archaeal lineages (ANME-1, ANME-2 and MBG-D), also suggest a potential connectivity among deep-sea ecosystems of the Guaymas Basin likely due to the sedimentary context and the absence of physical border. However, thermophilic and hyperthermophilic lineages (e.g. : Thermodesulfobacteria, Desulfurococcales, etc.) were exclusively identified in hydrothermally impacted sediments highlighting the strong influence of temperature gradients and other hydrothermally-related factors such as thermogenic sulfate reduction and sulfide formation on microbial community composition.

Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough

In this study, we analyzed the bacterial and archaeal diversities of the deep-sea sediments in Iheya North and Iheya Ridge, Okinawa Trough, using the high-throughput sequencing technology of Illumina MiSeq 2500 platform. Four samples (IN1, IN2, IR1 and IR2) were used in this study, of which IN1 and IN2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya North, while IR1 and IR2 were located at regions close to and distant, respectively, from the active hydrothermal vents in Iheya Ridge. The four samples were rich in different metal elements. Sequence analysis based on the V3–V4 regions of 16S rDNA gene obtained 170,363 taxon tags, including 122,920 bacterial tags and 47,433 archaeal tags, which cover 31 phyla, 50 classes, 59 orders, 87 families, and 138 genera. Overall, the microbial communities in all samples were dominated by bacteria, in which Proteobacteria was the largest phylum, followed by Chloroflexi, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae, which together accounted for 64.6% of the total taxon tags. In contrast to the high bacterial diversities, the archaeal diversity was low and dominated by Thaumarchaeota, which accounted for 22.9% of the total taxon tags. Comparative analysis showed that (i) IN2 and IR2 exhibited more microbial richness than IN1 and IR1, (ii) IR1 and IR2 exhibited higher microbial diversities than IN1 and IN2, (iii) samples from Iheya Ridge and Iheya North fell into two groups based on principle component analysis. Furthermore, microbes potentially involved in sulfur, nitrogen, and metal metabolism and cycling were detected in all samples. These results provide for the first time a comparative picture of the microbial diversities in the sediments of Iheya North and Iheya Ridge and indicate that geological features and distance from active hydrothermal vents likely play important roles in the shaping of microbial community structure.

象山港网箱养殖对近海沉积物细菌群落的影响

Microorganisms play important roles in biogeochemical cycling such as organic matter decomposition and energy transformation.Recently,rapid development of aquaculture has caused a large influx of introduced organic matter into Xiangshan Bay,Zhejiang Province,China.At the same time,many ecological problems have developed in this coastal site.Study of the influence of aquaculture on microbial diversity in sediments is important for the structural and functional assessment of coastal ecosystems.In this paper,sediments in three sites were investigated in July 2011: a control or check site(CK),an intersection site 6—8 km from the aquaculture site(IS),and a cage culture site(AC).As the physicochemical background showed,total organic carbon in those three sites was different.Several physiochemical factors(T,pH,Eh and SO2-4) were analyzed.The temperatures of sediments in Xiangshan Bay decreased with depth,but remained between 23.0—26.5 ℃ in the upper 55 cm layer.The pH of sediments was slightly alkaline,but was elevated slightly in the AC site,although all of the sediments had pH values of 7.6—7.9.The effect of aquaculture on SO2-4 was not significant.However,as expected,the measurement of Eh showed sediment in the CK site had the highest oxidation-reduction potential.Following with physiochemical analysis,the structure and diversity of bacterial communities in sediments from Xiangshan Bay were analyzed by Terminal Restriction Fragment Length Polymorphism(T-RFLP) analysis and cloning/sequencing.Total nucleic acids was extracted from the sediment core.T-RFLP analysis was conducted after amplification of the bacterial 16S rRNA partial gene using a fluorescent primer pair 27-FAM/907R and digestion by Msp I(C^CGG).A bacterial 16S rRNA partial gene clone library was constructed using DNA extracted from the upper 5 cm sediment layer of the CK region,and the phylogenic relationships were analyzed using the neighbor-joining method in ARB software.Our results revealed sediments from Xiangshan Bay had a highly diverse bacterial community,mainly including Proteobacteria,Firmicutes,Gemmatimonadetes,Actinobacteria,Thermomicrobia,Nitrospirae,Acidobacteria,Fusobacteria,Bacteroidetes,Planctomycetes and OP11.Thermomicrobia was the most abundant group in all sediments and layers,while the abundance of Proteobacteria was elevated in the surface layer of the CK site,making up as much as 23.7% of the clone library.The diversity index H′ is an effective method of assessing microbial diversity.In this study,the diversity index H′ was calculated based on T-RFLP relative abundance results.Generally,the bacterial diversity indices were CK IS AC.Surface layer sediments in the CK site showed the highest bacterial diversity(H′=3.83±0.01).The lowest diversity(H′=3.01±0.27) was in the 50—55 cm deep sediment in the AC site.The evenness indices were stable in the CK site(around 0.93),but also decreased in the AC site,especially in deeper layers.In the IS site,both diversity indices and evenness indices were intermediate between the CK and AC sites indicating the cage culture not only changed Eh and pH in sediments in Xiangshan Bay,but also decreased their bacterial diversity and changed the structure of the bacterial community.The bacterial community of coastal sediments was changing from a stable,highly diverse structure to an unstable structure with low diversity.Human activity such as aquaculture imports large amounts of organic matter,which not only modifies natural conditions but also leads to systemic simplification of the bacterial ecosystem.Sustainable and environmental friendly aquaculture methods should be searched for and found.

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany)

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity ( H′) ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites.

Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean

Cobalt-rich crusts are important metallic mineral resources with great economic potential, usually distributed on seamounts located in the Pacific Ocean. Microorganisms are believed to play a role in the formation of crusts as well as in metal cycling. To explore the microbial diversity related to cobalt-rich crusts, 16S ribosomal RNA gene clone libraries were constructed from three consecutive sediment layers. In total, 417 bacterial clones were obtained from three bacterial clone libraries, representing 17 distinct phylogenetic groups. Proteobacteria dominated in the bacterial communities, followed by Acidobacteria and Planctomycetes. Compared with high bacterial diversity, archaea showed a remarkably low diversity, with all 137 clones belonging to marine archaeal group I except one novel euryarchaeotal clone. The microbial communities were potentially involved in sulfur, nitrogen and metal cycling in the area of cobalt-rich crusts. Sulfur oxidation and metal oxidation were potentially major sources of energy for this ecosystem. This is the first reported investigation of microbial diversity in sediments associated with cobalt-rich crusts, and it casts fresh light on the microbial ecology of these important ecosystems.

Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea

Microbial diversity of sediments from the northern slope of the South China Sea was studied by constructing bacterial and archaeal 16S rRNA gene clone libraries. Fourteen bacterial phylogenetic groups were detected, including Gammaproteobacteria, Deltaproteobacteria, Planctomycetes, Alphaproteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Chloroflexi, Acidobacteria, Betaproteobacteria, Nitrospirae, candidate divisions OP8 and OP11, and an unknown group. Gammaproteobacteria was the predominant group in bacterial libraries with the percentage ranging from 31.8% to 63.2%. However, archaeal libraries had relatively lower diversity, with most clones belonging to marine archaeal group capital I, Ukrainian uncultured Crenarchaeota. In addition, two novel euryarchaeal clones were detected not to match any culture-dependent or -independent isolates. Compared with other gas hydrate-rich ecosystems and different areas of the South China Sea, a distinct microbial community was revealed in this study.

Effects of oxygenation on ammonia oxidation potential and microbial diversity in sediment from surface-flow wetland mesocosms

Addition of oxygen to surface-flow wetland mesocosms treating synthetic secondary effluent resulted in a significant increase in ammonia oxidation potential in sediment compared to non-oxygenated controls. Ammonia oxidation potential in oxygenated wetland sediment (1.2–3.5 mg N g dw −1 d −1) was 2–3 orders of magnitude higher than those measured in sediment and soil systems reported in the literature. Phylogenic analysis of sediment from the two treatments revealed substantial differences in microbial diversity including the presence of ammonia-oxidizing bacteria ( Nitrosomonas oligotropha) and denitrifying bacteria only in oxygenated sediment, and an increase in the diversity of aerobic phototrophs and methanotrophs in control sediment. These observations supported the contention by Palmer et al. (2009) that oxygenation ‘activated’ nitrifying bacteria in wetland sediment leading to high rates of biological ammonia oxidation.

Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin

A giant 800-m-diameter pockmark named REGAB was discovered on the Gabon continental margin actively emitting methane at a water depth of 3200 m. The microbial diversity in sediments from four different assemblages of chemosynthetic organisms, Mytilidae, Vesicomyidae, Sibogliniclae and a bacterial mat, was investigated using comparative 16S rRNA gene sequence analysis. Aggregates of anaerobic methanotrophic archaea (ANME-2) and bacteria of the Desulfosarcina/Desulfococcus cluster were found in all four chemosynthetic habitats. Fluorescence in situ hybridization targeting the ANME-2/Desulfosarcina/Desulfococcus aggregates showed their presence few centimeters (3-5cm) below the surface of sediment. 16S rRNA gene sequences from all known marine ANME groups were detected in the pockmark sediments, as well as from both known bacterial partners. The archaeal diversity was limited to the ANME cluster for all investigated samples. The bacterial diversity included members of the Proteobacteria, Bacilliales, Cytophaga/Flavobacteria, Verrucomicrobia, JS1 and Actinobacteria clusters. Bacterial 16S rRNA gene sequences related to those of known sulphide-oxidizing symbionts were recovered from tissues of several invertebrates including vesicomyid clams and siboglinid tubeworms of REGAB. (C) 2009 Elsevier Ltd. All rights reserved.