Spirosoma xylofaga sp. nov., an oligotrophic pleomorphic bacterium from a myco-bacterial community of freshwater ecosystems

ABSTRACT Freshwater ecosystems are exposed to multiple stressors, but their individual and combined effects remain largely unexplored. Here, we investigated the response of stream biofilm bacterial communities to warming, hydrological stress, and pesticide exposure. We used 24 artificial streams on which epilithic (growing on coarse sediments) and epipsammic (growing on fine sediments) stream biofilms were maintained. Bacterial community composition and estimated function of biofilms exposed during 30 days to individual and combined stressors were assessed using 16S rRNA gene metabarcoding. Among the individual effects by stressors, hydrological stress (i.e., a simulated low-flow situation) was the most relevant, since it significantly altered 57% of the most abundant bacterial taxa (n = 28), followed by warming (21%) and pesticide exposure (11%). Regarding the combined effects, 16% of all stressor combinations resulted in significant interactions on bacterial community composition and estimated function. Antagonistic responses prevailed (57 to 89% of all significant interactions), followed by synergisms (11 to 43%), on specific bacterial taxa, indicating that multiple-stressor scenarios could lead to unexpected shifts in the community composition and associated functions of riverine bacterial communities. IMPORTANCE Freshwater ecosystems such as rivers are of crucial importance for human well-being. However, human activities result in many stressors (e.g., toxic chemicals, increased water temperatures, and hydrological alterations) cooccurring in rivers and streams worldwide. Among the many organisms inhabiting rivers and streams, bacteria are ecologically crucial; they are placed at the base of virtually all food webs and they recycle the organic matter needed for bigger organisms. Most of these bacteria are in close contact with river substratum, where they form the biofilms. There is an urgent need to evaluate the effects of these stressors on river biofilms, so we can anticipate future environmental problems. In this study, we experimentally exposed river biofilms to a pesticide mixture, an increase in water temperature and a simulated low-flow condition, in order to evaluate the individual and joint effects of these stressors on the bacterial community composition and estimated function.

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Succession of Microbial Community in a Small Water Body within the Alluvial Aquifer of a Large River

Water ◽

10.3390/w13020115 ◽

2021 ◽

Vol 13 (2) ◽

pp. 115

Author(s):

Antonija Kulaš ◽

Tamara Marković ◽

Petar Žutinić ◽

Katarina Kajan ◽

Igor Karlović ◽

...

Keyword(s):

Bacterial Community ◽

Strong Correlation ◽

Algal Blooms ◽

Essential Elements ◽

Freshwater Ecosystems ◽

Alluvial Aquifer ◽

Winter Period ◽

Microbial Composition ◽

Small Water ◽

Interdisciplinary Approaches

Nitrogen is one of the essential elements limiting growth in aquatic environments. Being primarily of anthropogenic origin, it exerts negative impacts on freshwater ecosystems. The present study was carried out at the nitrate-vulnerable zone within the alluvial aquifer of the large lowland Drava River. The main aim was to investigate the ecosystem’s functionality by characterizing the bacterial and phytoplankton diversity of a small inactive gravel pit by using interdisciplinary approaches. The phytoplankton community was investigated via traditional microscopy analyses and environmental DNA (eDNA) metabarcoding, while the bacterial community was investigated by a molecular approach (eDNA). Variations in the algal and bacterial community structure indicated a strong correlation with nitrogen compounds. Summer samples were characterized by a high abundance of bloom-forming Cyanobacteria. Following the cyanobacterial breakdown in the colder winter period, Bacillariophyceae and Actinobacteriota became dominant groups. Changes in microbial composition indicated a strong correlation between N forms and algal and bacterial communities. According to the nitrogen dynamics in the alluvial aquifer, we emphasize the importance of small water bodies as potential buffer zones to anthropogenic nitrogen pressures and sentinels of the disturbances displayed as algal blooms within larger freshwater systems.

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Bacterial Community Composition in Oligosaline Lake Bosten: Low Overlap of Betaproteobacteria and Bacteroidetes with Freshwater Ecosystems

Microbes and Environments ◽

10.1264/jsme2.me14177 ◽

2015 ◽

Vol 30 (2) ◽

pp. 180-188 ◽

Cited By ~ 14

Author(s):

Xiangming Tang ◽

Guijuan Xie ◽

Keqiang Shao ◽

Jiangyu Dai ◽

Yuangao Chen ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Freshwater Ecosystems

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Assessments of Bacterial Community Shifts in Sediments along the Headwaters of São Francisco River, Brazil

Conservation ◽

10.3390/conservation1020008 ◽

2021 ◽

Vol 1 (2) ◽

pp. 91-105

Author(s):

Marcos de Paula ◽

Thiago Augusto Costa Costa Silva ◽

Amanda Soriano Araújo ◽

Gustavo Augusto Lacorte

Keyword(s):

Bacterial Community ◽

River Basin ◽

High Intensity ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Freshwater Ecosystems ◽

Community Diversity ◽

Anthropogenic Activity ◽

Sao Francisco River ◽

São Francisco River

Sustainable use of freshwater resources for human civilization needs requires the assessment and monitoring of freshwater health, and bacterial communities from riverbed sediments have been shown to be susceptible to chronic anthropogenic disturbances in freshwater ecosystems. Here, we took advantage of the occurrence of well-recognized adjacent sections from the Upper São Francisco River basin with well-recognized levels of anthropogenic activity intensity to test the applicability of sediment bacterial communities as bioindicators of impacts on freshwater ecosystems. We applied 16S amplicon sequencing to estimate the diversity and composition of bacterial communities from 12 sampling sites across the Upper São Francisco River basin, classified as being of no, low, or high intensity of anthropogenic activities, and used diversity metrics and LEfSe to compare the patterns of community structure. Our results revealed that accessed sediment environments associated with land areas with a high intensity of anthropogenic activities presented the lowest levels of community diversity, and the bacterial community compositions of these environments were significantly different from the other sampled areas. Our findings can be considered a source of evidence for the usefulness of bacterial community-based approaches as a tool for diagnosis and monitoring of ecosystem health in areas of vulnerable freshwater environments, and can even be incorporated into regular water quality programs.

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Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu

Water ◽

10.3390/w12020432 ◽

2020 ◽

Vol 12 (2) ◽

pp. 432

Author(s):

Yuanjiao LYU ◽

Rui Huang ◽

Jin Zeng ◽

Qinglong L. Wu

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Aquatic Macrophytes ◽

Riparian Zone ◽

Bacterial Community Composition ◽

Freshwater Ecosystems ◽

Riparian Zones ◽

Network Structures ◽

Bacterial Phyla ◽

Local Factors

Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the riparian zone as follows: The supralittoral and eulittoral zones with Phragmites australis, the eulittoral and infralittoral zones without P. australi. The bacterial communities in the four zones differed significantly based on taxonomic dissimilarity, but the two zones with P. australis exhibited phylogenetic closeness of the bacterial communities. The characteristics of the bacterial networks, such as connectivity, modularity, and topological roles of OTUs, were totally different between the P. australis and non-P. australis zones. Some bacterial phyla enriched in the P. australis zones were found to be putative keystone taxa in the networks, which might be involved in the regulation of bacterial interactions and plant growth. Moreover, the hydrological regime and particle size were shown to be determinants of the bacterial community and network structures in the riparian zones. In summary, our results show that the role of P. australis and local factors are crucial for constructing bacterial community and interactions in the riparian zones of lakes.

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Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis

Canadian Journal of Microbiology ◽

10.1139/w08-098 ◽

2008 ◽

Vol 54 (12) ◽

pp. 1053-1063 ◽

Cited By ~ 24

Author(s):

Jin Zeng ◽

Liu-Yan Yang ◽

Yi Liang ◽

Jia-Yun Li ◽

Lin Xiao ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Community Composition ◽

Eutrophic Lake ◽

Freshwater Ecosystems ◽

Scaling Analysis ◽

Gradient Gel Electrophoresis ◽

Lake Xuanwu

Bacterial community structure and the effects of several environmental factors on the microbial community distribution were investigated in the sediment of the eutrophic Lake Xuanwu. Profiles of bacterial communities were generated using denaturing gradient gel electrophoresis (DGGE), and the results were interpreted with multivariate statistical analysis. Five major variables in sediment were examined in a principal component analysis, which indicates notable differences of physicochemical parameters among different sites of the lake. To assess changes in the genetic diversity of bacterial communities of different sampling sites, DGGE band patterns were analyzed by multidimensional scaling analysis, which indicated that sampling sites having similar environmental characteristics also have the similar microbial communities. Canonical correspondence analysis demonstrated that pH and redox potential had significant effects on the bacterial community composition in the sediments. Analysis of DNA sequences revealed that the dominant bacterial groups in Lake Xuanwu belonged to Proteobacteria , Actinobacteria , Verrucomicrobia , and Nitrospirae , which are commonly isolated from freshwater ecosystems.

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Bacterial community structure and response to nitrogen amendments in Lake Shenandoah (VA, USA)

Water Science & Technology ◽

10.2166/wst.2019.311 ◽

2019 ◽

Vol 80 (4) ◽

pp. 675-684

Author(s):

G. Reynoso ◽

M. R. Smith ◽

C. P. Holmes ◽

C. R. Keelan ◽

S. E. McGrath ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Nitrogen Sources ◽

Amplicon Sequencing ◽

Freshwater Ecosystems ◽

Nitrogen Loading ◽

Significant Shift ◽

Nitrogen And Phosphorus ◽

The Impact

Abstract Microbial processes are critical to the function of freshwater ecosystems, yet we still do not fully understand the factors that shape freshwater microbial communities. Furthermore, freshwater ecosystems are particularly susceptible to effects of environmental change, including influx of exogenous nutrients such as nitrogen and phosphorus. To evaluate the impact of nitrogen loading on the microbial community structure of shallow freshwater lakes, water samples collected from Lake Shenandoah (Virginia, USA) were incubated with two concentrations of either ammonium, nitrate, or urea as a nitrogen source. The potential impact of these nitrogen compounds on the bacterial community structure was assessed via 16S rRNA amplicon sequencing. At the phylum level, the dominant taxa in Lake Shenandoah were comprised of Actinobacteria and Proteobacteria, which were not affected by exposure to the various nitrogen treatments. Overall, there was not a significant shift in the diversity of the bacterial community of Lake Shenandoah with the addition of nitrogen sources, indicating this shallow system may be constrained by other environmental factors.

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Assessment of viral assemblages in different types of wetland water in northeast China using RAPD-PCR

Aquatic Microbial Ecology ◽

10.3354/ame01952 ◽

2020 ◽

Vol 85 ◽

pp. 183-196

Author(s):

Y Sun ◽

J Liu ◽

Q Yao ◽

J Jin ◽

X Liu ◽

...

Keyword(s):

Bacterial Community ◽

Water Samples ◽

Northeast China ◽

Bacterial Community Composition ◽

Freshwater Wetlands ◽

Viral Community ◽

Rapd Pcr ◽

Wetland Water ◽

Different Types ◽

Viral Communities

Viruses are the most abundant and ubiquitous biological entities in various ecosystems, yet few investigations of viral communities in wetlands have been performed. To address this data gap, water samples from 6 wetlands were randomly collected across northeast China; viruses in the water were concentrated by sequential tangential flow filtration, and viral communities were assessed through randomly amplified polymorphic DNA-PCR (RAPD-PCR) with 4 decamer oligonucleotide primers. Principal coordinate analysis and hierarchical clustering analysis of the DNA fingerprints showed that viral community compositions differed among the water samples: communities in the 2 coastal wetlands were more similar to each other than to those in the 4 freshwater wetlands. The Shannon-Weaver index (H) and evenness index (E) of the RAPD-PCR fingerprint also differed among the 6 wetlands. Mantel test revealed that the changes in viral communities in wetland water were most closely related to the water NH4+-N and inorganic C content, followed by total K, P, C and NO3--N. DNA sequence analysis of the excised bands revealed that viruses accounted for ~40% of all sequences. Among the hit viral homologs, the majority belonged to the Microviridae. Moreover, variance partitioning analysis showed that the viral community contributed 24.58% while environmental factors explained 30.56% of the bacterial community variation, indicating that the bacterial community composition was strongly affected by both viral community and water variables. This work provides an initial outline of the viral communities from different types of wetlands in northeast China and improves our understanding of the viral diversity in these ecosystems.

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