Diversity In Surface Sediments Research Articles

Spatiotemporal patterns and co-occurrence patterns of dissimilatory nitrate reduction to ammonium community in sediments of the Lancang River cascade reservoirs.

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate reduction pathway in freshwater sediments. Many studies have focused on the DNRA process in various natural habitats. However, the joint operation of cascade reservoirs will affect the physical and chemical properties of sediments, which may change the DNRA process and bacterial community pattern in the surface sediments of cascade reservoirs. Our study was the first to investigate the spatiotemporal distribution patterns of potential DNRA rate, nrfA gene abundances, and DNRA bacterial community diversity in surface sediments of the Lancang River cascade reservoirs. The results of slurry incubation experiments combined with the 15N isotope tracer experiment ascertained that the potential rates of DNRA were 0.01-0.15 nmol-N cm-3 h-1, and qPCR results indicated that the abundance range of nrfA was 1.08 × 105-2.51 × 106 copies g-1 dry weight. High throughput sequencing of the nrfA gene revealed that the relative abundance of Anaeromyxobacter (4.52% on average), Polyangium (4.09%), Archangium (1.86%), Geobacter (1.34%), and Lacunisphaera (1.32%) were high. Pearson and RDA correlation analysis exhibited that nrfA gene abundance was positively correlated with altitude, pH, OC, and sand concentration. Anaeromyxobacter was positively correlated with reservoir age and DNRA potential rate. The deterministic environmental selection process plays a crucial role in the formation of the DNRA bacterial community. Network analysis displayed that the dominant DNRA genus was the key population of the DNRA microbial community in the sediments of Lancang River cascade reservoirs. This study reveals that the variation of DNRA bacterial activity and community structure is largely driven by the construction of cascade reservoirs, and provides a new idea for further understanding the characteristics of the DNRA community in the cascade reservoir ecosystem.

Structural Diversity of Bacterial Communities and Its Relation to Environmental Factors in the Surface Sediments from Main Stream of Qingshui River

This paper aims to preliminarily understand the structure and diversity of the bacterial community in the sediments of the Qingshui River, and analyze the differences of dominant bacteria in different river reaches, and identify the influence degree of environmental factors. In this study, surface sediments of the main stream of the Qingshui River were selected to analyze both bacterial community composition and a diversity index using the high-throughput sequencing analysis of bacterial 16S rDNA, further exploring their relationships with environmental factors. Results showed that 16,855 OTUs in the surface sediments belonged to 66 phyla, 164 classes, 274 orders, 317 families, and 501 genera of bacteria, while carbon/nitrogen-fixing bacteria were dominant at the class and genus level. There was a significant (p < 0.05) spatial difference between bacterial species composition and the diversity index in surface sediments. Proteobacteria was the most abundant phylum in the sediments of the main stream of the Qingshui River, with an average abundance of 48.15%, followed by Bacteroidetes (21.74%) and Firmicutes (5.71%). The abundance of Alphaproteobacteria in Proteobacteria was the highest (15.38%) and followed by Flavobacteriia in Bacteroidetes (11.57%). The most dominant bacteria genera were different at different areas. The most dominant genera were Phyllobacterium in Kaicheng, Qiying, Liwang, Tongxin and Changshantou, with relative abundances of 4.27%, 4.67%, 5.88%, 4.15% and 6.22%, respectively. Flavobacterium was the most dominant genus in both Dongjiao and Sanying, with a relative abundance of 5.03% and 5.84%, respectively. Rhodobacter was the most dominant genus in Hexi, with a relative abundance of 8.29%. Gillisia was the most dominant genus in Quanyanshan, with a relative abundance of 5.51%. Pearson correlation analysis further indicated that NH4+, pH, and Cr were the main factors affecting the bacterial community structure and diversity in surface sediments. Therefore, our findings suggest that both nutrient elements (i.e., N) and toxic heavy metalloids affect the abundance and diversity of bacteria in surface sediments from the main stream of the Qingshui River. Areas of the river sampled in this study provide the biggest microbial sampling coverage to date. The results provide a preliminary understanding of bacterial communities in sediments of different reaches of the Qingshui River, and provide a reference for further research on the application of functional bacteria in pollution control of the Qingshui River.

Bacterial diversity in surface sediments of collapsed lakes in Huaibei, China

The collapse lake area due to coal mining in Huaibei shows high biodiversity, but the bacterial community composition and diversity in the lake sediments are still rarely studied. Therefore, based on 16S rRNA high-throughput sequencing and combined with analysis of environmental factors, we comparatively analyzed the bacterial community composition and diversity of surface sediments from East Lake (DH) and South Lake (NH) and Middle Lake (ZH) in the collapse lake area of Huaibei. The bacterial community compositions are significantly different in the sediments among Huaibei collapsed lakes, with DH having the largest number of species, and NH having a higher species diversity. Pseudomonadota is the most abundant phylum in the sediments of DH and NH, while the most abundant phyla in ZH are Bacteroidales, Chloroflexales, Acidobacteriales, and Firmicutes. Anaerolineae (24.05% ± 0.20%) is the most abundant class in the DH sediments, and Gammaproteobacteria (25.94% ± 0.40%) dominates the NH sediments, Bacteroidia (32.12% ± 1.32%) and Clostridia (21.98% ± 0.90%) contribute more than 50% to the bacteria in the sediments of ZH. Redundancy analysis (RDA) shows that pH, TN, and TP are the main environmental factors affecting the bacterial community composition in the sediments of the collapsed lake area. The results reveal the bacterial community composition and biodiversity in the sediments of the Huaibei coal mining collapsed lakes, and provide new insights for the subsequent ecological conservation and restoration of the coal mining collapsed lakes.

Bacterial diversity in surface sediments from the continental shelf and slope of the North West gulf of Mexico and the presence of hydrocarbon degrading bacteria.

Bacteria play an important role in ecological processes in oil contaminated marine sediments. In this work, bacterial diversity studies with surface sediment samples from the NW Gulf of Mexico were performed, two from continental shelf and two from upper slope. The bacterial communities seem significantly influenced by depth, distance from the shoreline, temperature, dissolved oxygen and aluminum. The most abundant Phylum was Proteobacteria, Class Gammaproteobacteria. However, Class Deltaproteobacteria, Order Desulfuromonadales predominated in continental shelf and Order Alteromonadales (Gammaproteobacteria) prevailed in the upper slope sediments. Many potential hydrocarbon degrading bacterial genera were identified, 71 of the assigned genera were associated to hydrocarbon degradation processes. The genera Desulfobulbus and Haliea were confined to continental inner-shelf, while Shewanella and Fusibacter were mostly detected in deeper sediments. The occurrence and abundance of putative hydrocarbon degrading bacteria in this area, could be indicative of an impacted zone caused by the presence hydrocarbons in the environment.

Potential recycling of thaumarchaeotal lipids by DPANN Archaea in seasonally hypoxic surface marine sediments

Thaumarchaeota synthesize specific glycerol dibiphytanyl glycerol tetraethers (GDGTs), the distribution of which is affected by temperature, thereby forming the basis of the paleotemperature proxy, TEX86. Lipids in marine surface sediments are believed to be derived mainly from pelagic Thaumarchaeota; however, some studies have evaluated the possibility that benthic Archaea also contribute to the lipid fossil record. Here, we compared the archaeal abundance and composition from DNA-based methods with the archaeal intact polar lipid (IPL) diversity in surface sediments of a seasonally hypoxic marine lake to determine the potential biological sources of the sedimentary archaeal IPLs under changing environmental conditions. The archaeal community changed from March (oxic conditions) to August (euxinic) from a Thaumarchaeota-dominated community (up to 82%) to an archaeal community dominated by the DPANN super phylum (up to 95%). This marked change coincided with a one order of magnitude decrease in the total IPL-GDGT abundance. In addition, IPL-GDGTs with a glyco polar head group increased. This may indicate a transition to Thaumarchaeota growing in stationary phase or selective preservation of the GDGT pool. In addition, considering the apparent inability of the DPANN Archaea to synthesize their own membrane lipids, we hypothesize that the dominant DPANN Archaea population present in August use the lipids synthesized previously by the Thaumarchaeota or other Archaea to form their own cell membranes, which would indicate an active recycling of fossil IPLs in the marine surface sediment.

Insights into the diversity and metabolic function of bacterial communities in sediments from Chilean salmon aquaculture sites

Aquaculture is an extremely valuable and rapidly expanding sector worldwide, but concerns exist related to environmental sustainability. The sediment below aquaculture farms receives inputs of antimicrobials, metal-containing products, and organic matter from uneaten food and fecal material. These inputs impact the surrounding marine microbial communities in complex ways; however, functional diversity shifts related to taxonomic composition remain poorly understood. Here, we investigated the effect of pollution from marine fish farms on sediment bacterial communities. We compared the bacterial communities and functional bacterial diversity in surface sediments at salmon aquaculture and reference sites in Chiloe, southern Chile, using Roche 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene and the predictive metagenomics approach (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt). Bacterial diversity, measured as the inverse Simpson index, was significantly lower at aquaculture than at reference sites, while species richness, based on Chao’s estimator, was not significantly different. Nevertheless, community composition differed significantly between reference and aquaculture sites. We found that Gammaproteobacteria and several taxa involved in remediating metal contamination and known to have antimicrobial resistances were enriched at aquaculture sites. However, PICRUSt predicted functions indicated a degree of functional redundancy between sites, whereas taxonomic-functional relationships indicated differences in the functional traits of specific taxa at aquaculture sites. This study provides a first step in understanding the bacterial community structure and functional changes due to Chilean salmon aquaculture and has direct implications for using bacterial shifts as indicators of aquaculture perturbations.

An insight into the feeding ecology of deep-sea canyon nematodes — Results from field observations and the first in-situ13C feeding experiment in the Nazaré Canyon

Submarine canyon systems provide a heterogeneous habitat for deep-sea benthos in terms of topography, hydrography, and the quality and quantity of organic matter present. Enhanced meiofauna densities as found in organically enriched canyon sediments suggest that nematodes, as the dominant metazoan meiobenthic taxon, may play an important role in the benthic food web of these sediments. Very little is known about the natural diets and trophic biology of deep-sea nematodes, but enrichment experiments can shed light on nematode feeding selectivity and trophic position. An in-situ pulse-chase experiment (Feedex) was performed in the Nazaré Canyon on the Portuguese margin in summer 2007 to study nematode feeding behaviour. 13C-labelled diatoms and bacteria were added to sediment cores which were then sampled over a 14-day period. There was differential uptake by the nematode community of the food sources provided, indicating selective feeding processes. 13C isotope results revealed that selective feeding was less pronounced at the surface, compared to the sediment subsurface. This was supported by a higher trophic diversity in surface sediments (Θ−1=3.50±0.2) compared to the subsurface (2.78±0.6), implying that more food items may be used by the nematode community at the sediment surface. Predatory and scavenging nematodes contributed relatively more to biomass than other feeding types and can be seen as key contributors to the nematode food web at the canyon site. Non-selective deposit feeding nematodes were the dominant trophic group in terms of abundance and contributed substantially to total nematode biomass. The high levels of ‘fresh’ (bioavailable) organic matter input and moderate hydrodynamic disturbance of the canyon environment lead to a more complex trophic structure in canyon nematode communities than that found on the open continental slope, and favours predator/scavengers and non-selective deposit feeders.

Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments

Bioturbation is a key process in coastal sediments, influencing microbially driven cycling of nutrients as well as the physical characteristics of the sediment. However, little is known about the distribution, diversity and function of the microbial communities that inhabit the burrows of infaunal macroorganisms. In this study, terminal-restriction fragment length polymorphism analysis was used to investigate variation in the structure of bacterial communities in sediment bioturbated by the burrowing shrimp Upogebia deltaura or Callianassa subterranea. Analyses of 229 sediment samples revealed significant differences between bacterial communities inhabiting shrimp burrows and those inhabiting ambient surface and subsurface sediments. Bacterial communities in burrows from both shrimp species were more similar to those in surface-ambient than subsurface-ambient sediment (R=0.258, P<0.001). The presence of shrimp was also associated with changes in bacterial community structure in surrounding surface sediment, when compared with sediments uninhabited by shrimp. Bacterial community structure varied with burrow depth, and also between individual burrows, suggesting that the shrimp's burrow construction, irrigation and maintenance behaviour affect the distribution of bacteria within shrimp burrows. Subsequent sequence analysis of bacterial 16S rRNA genes from surface sediments revealed differences in the relative abundance of bacterial taxa between shrimp-inhabited and uninhabited sediments; shrimp-inhabited sediment contained a higher proportion of proteobacterial sequences, including in particular a twofold increase in Gammaproteobacteria. Chao1 and ACE diversity estimates showed that taxon richness within surface bacterial communities in shrimp-inhabited sediment was at least threefold higher than that in uninhabited sediment. This study shows that bioturbation can result in significant structural and compositional changes in sediment bacterial communities, increasing bacterial diversity in surface sediments and resulting in distinct bacterial communities even at depth within the burrow. In an area of high macrofaunal abundance, this could lead to alterations in the microbial transformations of important nutrients at the sediment-water interface.

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

In order to assess bacterial diversity within four surface sediment samples (0-5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (alpha, beta, gamma, delta and epsilon-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). alpha, gamma, and delta-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The gamma-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of gamma-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.

Microbial diversity in surface sediments of the Xisha Trough, the South China Sea

Microbial communities were obtained from the surface sediments of the Xisha Trough using the culture-independent technique. The characteristics of the 16S rDNA gene amplified from the sediments indicated that archaeal clones could be grouped into Euryarchaeota and Crenarchaeota, respectively. Two archaeal groups, Marine Crenarchaeotic Group I and Terrestrial Miscellaneous Euryarchaeotal Group, were the most dominant archaeal 16S rDNA gene components in the sediments. The remaining components were related to the members of Marine Benthic Group B, Marine Benthic Group A, Marine Benthic Group D, Novel Euryarchaeotic Group and C3. The bacterial clones exhibited greater diversity than the archaeal clones with the 16S rDNA gene sequences from the members of Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, candidate division OP8, Bacterioidetes/Chlorobi and Verrucomicrobia. Most of these lineages represented uncultured microorganisms. The result suggests that a vast amount of microbial resource in the surface sediments of the South China Sea has not been known.

Palaeoecological perspectives on pattern and process in plant diversity and distribution adjustments: a comment on recent developments*

Abstract.Two developments in the understanding of the relationship between sedimentary pollen assemblages, vegetation and plant diversity are discussed. The Prentice model of vegetation–pollen relationships has improved our understanding of how and at what scale sedimentary pollen records vegetation. The modelling framework allows improved palaeoecological study designs that may, potentially, give important new insights into processes of plant migrations in response to climate change. Also, reconstructions of plant communities and landscape openness may be improved. Competing hypotheses for the relationship between vegetation and palynological diversity are discussed and it is concluded that more attention should be focused on evenness aspects of palynological diversity and on hypothesis testing.

Patterns of planktonic foraminiferal abundance and diversity in surface sediments of the western North Atlantic

Seventy-two core tops and grab samples from the western North Atlantic were analyzed to determine what aspects of planktonic foraminiferal abundance and diversity are most closely related to ocean circulation. Some species appear to be reliable indicators of the Gulf Stream, a warm surface current. Both Globorotalia menardii and Globigerinoides sacculifer have their highest abundances under the main trend of the Gulf Stream. Globorotalia inflata reaches high abundances in the cold slope water north of the Gulf Stream but its distribution is not as continuous as the Gulf Stream indicators. Contoured values of species diversity, the Shannon diversity index, and species equitability also reflect surface circulation. A plot of species diversity (number of species) shows a poorly defined region of high diversity beneath the major trend of the Gulf Stream. Use of the Shannon diversity index enhances and clarifies this region of high diversity. A map of species equitability shows a broad belt of low species dominance (high equitability) beneath the Gulf Stream. North of the Gulf Stream, a tongue of high dominance (low equitability) corresponds to the increased relative abundance of Globorotalia inflata. High diversity of planktonic foraminifera in bottom sediments characterizes the warm shifting surface currents of the Gulf Stream; low diversity is typical of slope and Sargasso Sea waters. Low equitability (high species dominance) indicates either cold currents or gyre center waters. Maps of foraminiferal diversity and equitability for other intervals of geologic time may be useful in tracing the evolution of ocean circulation.