scholarly journals Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients

2022 ◽  
Vol 12 ◽  
Author(s):  
Marie-Amélie Blais ◽  
Alex Matveev ◽  
Connie Lovejoy ◽  
Warwick F. Vincent
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Environmental Gradients ◽  
Size Fraction ◽  
Rrna Genes ◽  
Small Rivers ◽  
Hudson Bay ◽  
Core Microbiome ◽  
Pigment Analysis

Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.

scholarly journals Bioaugmentation of Activated Sludge by an Indigenous 3-Chloroaniline-Degrading Comamonas testosteroni Strain, I2gfp

2000 ◽  
Vol 66 (7) ◽  
pp. 2906-2913 ◽  
Author(s):  
Nico Boon ◽  
Johan Goris ◽  
Paul De Vos ◽  
Willy Verstraete ◽  
Eva M. Top
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Activated Sludge ◽  
Microbial Community Structure ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dynamic Change ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Adaptation Period ◽  
Comamonas Testosteroni

ABSTRACT A strain identified as Comamonas testosteroni I2 was isolated from activated sludge and found to be able to mineralize 3-chloroaniline (3-CA). During the mineralization, a yellow intermediate accumulated temporarily, due to the distalmeta-cleavage of chlorocatechol. This strain was tested for its ability to clean wastewater containing 3-CA upon inoculation into activated sludge. To monitor its survival, the strain was chromosomally marked with the gfp gene and designated I2gfp. After inoculation into a lab-scale semicontinuous activated-sludge (SCAS) system, the inoculated strain maintained itself in the sludge for at least 45 days and was present in the sludge flocs. After an initial adaptation period of 6 days, complete degradation of 3-CA was obtained during 2 weeks, while no degradation at all occurred in the noninoculated control reactor. Upon further operation of the SCAS system, only 50% 3-CA removal was observed. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes revealed a dynamic change in the microbial community structure of the activated sludge. The DGGE patterns of the noninoculated and the inoculated reactors evolved after 7 days to different clusters, which suggests an effect of strain inoculation on the microbial community structure. The results indicate that bioaugmentation, even with a strain originating from that ecosystem and able to effectively grow on a selective substrate, is not permanent and will probably require regular resupplementation.

scholarly journals Unexpected Diversity during Community Succession in the Apple Flower Microbiome

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Ashley Shade ◽  
Patricia S. McManus ◽  
Jo Handelsman
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Disease Management ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Local Similarity ◽  
Ecological Understanding ◽  
Culture Independent

ABSTRACTDespite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 andDeinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management.IMPORTANCEFlowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated withDeinococcus-Thermusand TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.

scholarly journals Microbial community structure and diversity within hypersaline Keke Salt Lake environments

2017 ◽  
Vol 63 (11) ◽  
pp. 895-908 ◽  
Author(s):  
Rui Han ◽  
Xin Zhang ◽  
Jing Liu ◽  
Qifu Long ◽  
Laisheng Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Salt Lake ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Tibet Plateau ◽  
Hypersaline Lake ◽  
Hypersaline Lakes

Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3–V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%–58.35% relative abundance), Lactococcus (9.52%–10.51%), and Oceanobacillus (8.82%–9.88%) within the Firmicutes phylum (74.81%–80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai–Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl–, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.

scholarly journals Soil biological characteristics and microbial community structure in a field experiment

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Olga Mikanová ◽  
Tomáš Šimon ◽  
Jan Kopecký ◽  
Markéta Ságová-Marečková
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Field Experiment ◽  
Microbial Community Structure ◽  
Farmyard Manure ◽  
Biological Characteristics ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Mineral Fertilizers ◽  
Cattle Slurry

AbstractThe influence of different fertilization treatments on soil biological characteristics and microbial community structure was investigated. Soil samples were taken from a long-term field experiment which was conducted to explore the effect of eight treatments: control (non-fertilized), NPK (nitrogen, phosphorus and potassium), FYM (farmyard manure), FYM + NPK, CSl + St (cattle slurry + straw), CSl + St + NPK, CSl, CSl + NPK. The highest values of invertase activity were found in treatment fertilized with farmyard manure combined mineral fertilizers, similarly to total N content, activity of urease, and C of microbial biomass. Dehydrogenase activity was lower in all treatments with mineral fertilization. Bacterial and actinobacterial T-RFLP profiles of 16S rRNA genes showed similar patterns in response to eight fertilization treatments. In both, the communities formed distinct groups, which were separated by organic fertilization i.e. cattle slurry and straw amendments along the x axes and by NPK amendments along the y axes using the Sammon’s method of multidimensional scaling. Significant correlations were determined in several situations related to diversity: between invertase and 1/Db (dominance, bacteria), 1/Da (dominance, actinobacteria) and between T-RFLP profiles of actinobacteria, nitrogen and organic carbon content and bacterial E (evenness).

The First Use of Biofilm Microbial Community Structure as an Indicator of Impact of Two Dams on the Elwha River (Washington)

2009 ◽  
Vol 27 (4) ◽  
pp. 385-387
Author(s):  
W. D. Eaton ◽  
B. Wilmot ◽  
E. Epler ◽  
S. Mangiamelli ◽  
D. Barry
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Elwha River
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