scholarly journals Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change

2005 ◽  
Vol 71 (8) ◽  
pp. 4364-4371 ◽  
Author(s):  
Hermanni Kaartokallio ◽  
Maria Laamanen ◽  
Kaarina Sivonen
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
Sea Ice ◽  
Baltic Sea ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Bacterial Abundance ◽  
Open Water ◽  
Salinity Change

ABSTRACT To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.

scholarly journals Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

2013 ◽  
Vol 10 (4) ◽  
pp. 2747-2759 ◽  
Author(s):  
E. Ortega-Retuerta ◽  
F. Joux ◽  
W. H. Jeffrey ◽  
J. F. Ghiglione
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
Surface Waters ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Canadian Arctic ◽  
Beaufort Sea ◽  
Free Living ◽  
Open Sea

Abstract. We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea in the Canadian Arctic Ocean, with a particular focus on free-living (FL) vs. particle-attached (PA) communities. Capillary electrophoresis–single-strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between PA and FL bacterial community structure in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (a proxy of dissolved organic carbon and chromophoric dissolved organic matter), suspended particles, amino acids and chlorophyll a. Pyrosequencing of 16S rRNA genes from selected samples confirmed significant differences between river, coastal and sea samples. The PA fraction was only different (15.7% similarity) from the FL one in the open sea sample. Furthermore, PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, for the coast and river samples and both PA and FL fractions, Betaproteobacteria, Alphaproteobacteria and Actinobacteria were dominant. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particle loads.

scholarly journals Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice

2021 ◽  
Author(s):  
◽  
Rebecca Olivia MacLennan Cowie
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sea Ice ◽  
Structure Function ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Ice Thickness ◽  
Sea Ice Thickness ◽  
Antarctic Sea Ice ◽  
The Antarctic

<p>Antarctic sea ice is an important feature of the southern ocean where at its maximum it can cover 8 % of the Southern Hemisphere. It provides a stable environment for the colonisation of diverse and highly specialised microbes which play a central role in the assimilation and regulation of energy through the Antarctic food web. Polar environments are sensitive to changes in the environment. Small changes in temperature can have large effects on sea ice thickness and extent and Antarctic sea ice cover is expected to shrink by 25 % over the next century. It is unknown how the sea ice microbiota will respond. In order to understand the effects of climate change on the sea ice ecosystem it is necessary to obtain information about the community structure, function and diversity and their reactions with the environment. Studies have focused on algal diversity and physiology in Antarctic sea ice and in comparison studies on the prokaryotic community are few. Although prokaryotic diversity has been investigated using clone libraries and culture based methods, it is likely that certain species have still not been described. Almost nothing is known about the Antarctic sea ice bacterial community spatial and temporal dynamics under changing abiotic and biotic conditions or their role in biogeochemical cycles. This is the first study linking Antarctic bacterial communities to function by using statistics to investigate the relationships between environmental variables and community structure. Bacterial community structure was investigated by extracting both the DNA and RNA from the environment to understand both the metabolically active (RNA) and total (DNA) bacterial community. The thickness of the sea ice and nutrient concentrations were key factors regulating bacterial community composition in Antarctic sea ice. Sea ice thickness is likely to have an effect on the physiological responses of algae leading to changes in photosynthate concentrations and composition of dissolved organic matter (DOM). Further investigations into the relationships between enzymatic activity and community structure revealed that the composition of the DOM drove variation between bacterial communities. There was no relationship between bacterial abundance and chlorophyll-a (as a measure of algal biomass), suggesting a un-coupling of the microbial loop. However bacteria were actively involved in the hydrolysis of polymers throughout the sea ice core. Investigations using quantitative PCR (qPCR) found that the functional genes involved in denitrification and light energy utilisation were in low abundance therefore these processes are minor in Antarctic sea ice. These results confirm that sea ice bacteria are predominantly heterotrophs and have a major role in the cycling of carbon and nitrogen through the microbial loop ...</p>

scholarly journals Bacterial Community Structure, Function and Diversity in Antarctic Sea Ice

2021 ◽  
Author(s):  
◽  
Rebecca Olivia MacLennan Cowie
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Sea Ice ◽  
Structure Function ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Ice Thickness ◽  
Sea Ice Thickness ◽  
Antarctic Sea Ice ◽  
The Antarctic

<p>Antarctic sea ice is an important feature of the southern ocean where at its maximum it can cover 8 % of the Southern Hemisphere. It provides a stable environment for the colonisation of diverse and highly specialised microbes which play a central role in the assimilation and regulation of energy through the Antarctic food web. Polar environments are sensitive to changes in the environment. Small changes in temperature can have large effects on sea ice thickness and extent and Antarctic sea ice cover is expected to shrink by 25 % over the next century. It is unknown how the sea ice microbiota will respond. In order to understand the effects of climate change on the sea ice ecosystem it is necessary to obtain information about the community structure, function and diversity and their reactions with the environment. Studies have focused on algal diversity and physiology in Antarctic sea ice and in comparison studies on the prokaryotic community are few. Although prokaryotic diversity has been investigated using clone libraries and culture based methods, it is likely that certain species have still not been described. Almost nothing is known about the Antarctic sea ice bacterial community spatial and temporal dynamics under changing abiotic and biotic conditions or their role in biogeochemical cycles. This is the first study linking Antarctic bacterial communities to function by using statistics to investigate the relationships between environmental variables and community structure. Bacterial community structure was investigated by extracting both the DNA and RNA from the environment to understand both the metabolically active (RNA) and total (DNA) bacterial community. The thickness of the sea ice and nutrient concentrations were key factors regulating bacterial community composition in Antarctic sea ice. Sea ice thickness is likely to have an effect on the physiological responses of algae leading to changes in photosynthate concentrations and composition of dissolved organic matter (DOM). Further investigations into the relationships between enzymatic activity and community structure revealed that the composition of the DOM drove variation between bacterial communities. There was no relationship between bacterial abundance and chlorophyll-a (as a measure of algal biomass), suggesting a un-coupling of the microbial loop. However bacteria were actively involved in the hydrolysis of polymers throughout the sea ice core. Investigations using quantitative PCR (qPCR) found that the functional genes involved in denitrification and light energy utilisation were in low abundance therefore these processes are minor in Antarctic sea ice. These results confirm that sea ice bacteria are predominantly heterotrophs and have a major role in the cycling of carbon and nitrogen through the microbial loop ...</p>

scholarly journals Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1465
Author(s):  
Chao Shen ◽  
Liuyan Huang ◽  
Guangwu Xie ◽  
Yulai Wang ◽  
Zongkai Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Diversity Index ◽  
Plastic Substrate ◽  
Simpson Index ◽  
Plastic Debris ◽  
Plastic Substrates ◽  
Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 701 ◽  
Author(s):  
Fengling Zhang ◽  
Xingjia Xiang ◽  
Yuanqiu Dong ◽  
Shaofei Yan ◽  
Yunwei Song ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Stopover Site ◽  
Intestinal Bacterial Community ◽  
Hooded Crane ◽  
Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

scholarly journals Comparative analysis of the composition of bacterial communities from two constructed wetlands for municipal and swine wastewater treatment

2009 ◽  
Vol 8 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Paula Arroyo ◽  
Gemma Ansola ◽  
Ivan Blanco ◽  
Patricia Molleda ◽  
Estanislao de Luis Calabuig ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Typha Latifolia ◽  
Treatment System ◽  
Swine Wastewater ◽  
Wastewater Treatment System ◽  
Wastewater Treatment Systems

This work provides information about bacterial community structure in natural wastewater treatment systems treating different types of wastewater. The diversity and composition of bacterial communities associated with the rhizosphere of Typha latifolia and Salix atrocinerea were studied and compared among two different natural wastewater treatment systems, using the direct sequencing of the 16S ribosomal RNA codifying genes. Phylogenetic affiliations of the bacteria detected allowed us to define the main groups present in these particular ecosystems. Moreover, bacterial community structure was studied through two diversity indices. Ten identified and five non-identified phyla were found in the samples; the phylum Proteobacteria was the predominant group in the four ecosystems. The results showed a bacterial community dominated by beta-proteobacteria and a lower diversity value in the swine wastewater treatment system. The municipal wastewater treatment system presented a high diverse community in both macrophytes (Typha latifolia and Salix atrocinerea), with gamma-proteobacteria and alpha-proteobacteria, respectively, as the most abundant groups.

scholarly journals Effect of Wastewater Treatment Plant Effluent on Microbial Function and Community Structure in the Sediment of a Freshwater Stream with Variable Seasonal Flow

2008 ◽  
Vol 74 (9) ◽  
pp. 2659-2668 ◽  
Author(s):  
Steven A. Wakelin ◽  
Matt J. Colloff ◽  
Rai S. Kookana
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
Wastewater Treatment Plant ◽  
Bacterial Communities ◽  
Nutrient Loading ◽  
Treatment Plant ◽  
Biogeochemical Cycling ◽  
Rrna Genes

ABSTRACT We investigated the effects of wastewater treatment plant (WWTP) discharge on the ecology of bacterial communities in the sediment of a small, low-gradient stream in South Australia. The quantification of genes involved in the biogeochemical cycling of carbon and nitrogen was used to assess potential impacts on ecosystem functions. The effects of disturbance on bacterial community structure were assessed by PCR-denaturing gradient gel electrophoresis of 16S rRNA genes, and clone library analysis was used to phylogenetically characterize significant shifts. Significant (P < 0.05) shifts in bacterial community structures were associated with alteration of the sediment's physicochemical properties, particularly nutrient loading from the WWTP discharge. The effects were greatest at the sampling location 400 m downstream of the outfall where the stream flow is reduced. This highly affected stretch of sediment contained representatives of the gammaproteobacteria that were absent from less-disturbed sites, including Oceanospirillales and Methylococcaceae. 16S rRNA gene sequences from less-disturbed sites had representatives of the Caulobacteraceae, Sphingomonadaceae, and Nitrospirae which were not represented in samples from disturbed sediment. The diversity was lowest at the reference site; it increased with proximity to the WWTP outfall and declined toward highly disturbed (400 m downstream) sites (P < 0.05). The potential for biological transformations of N varied significantly with the stream sediment location (P < 0.05). The abundance of amoA, narG, and nifH genes increased with the distance downstream of the outfall. These processes are driven by N and C availability, as well as redox conditions. Together these data suggest cause and effect between nutrient loading into the creek, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of N.

scholarly journals Ice formation and growth shape bacterial community structure in Baltic Sea drift ice

2014 ◽  
Vol 91 (2) ◽  
pp. 1-13 ◽  
Author(s):  
Eeva Eronen-Rasimus ◽  
Christina Lyra ◽  
Janne-Markus Rintala ◽  
Klaus Jürgens ◽  
Vilma Ikonen ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Baltic Sea ◽  
Bacterial Community Structure ◽  
Ice Formation ◽  
Growth Shape
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