Microbial community structure and trichloroethylene degradation in groundwater

2005 ◽  
Vol 51 (6) ◽  
pp. 433-439 ◽  
Author(s):  
J A Humphries ◽  
A M.H Ashe ◽  
J A Smiley ◽  
C G Johnston
Keyword(s):  
Community Structure ◽  
Clone Library ◽  
Sequence Data ◽  
Restriction Analysis ◽  
Diversity Indices ◽  
Department Of Energy ◽  
Tetrazolium Chloride ◽  
Degrading Bacteria ◽  
Trichloroethylene Degradation ◽  
Rdna Clone

Trichloroethylene (TCE) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. Groundwater contaminated with TCE from a US Department of Energy site in Ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. Incubations of14C-TCE-spiked groundwater amended with phenol showed increased TCE mineralization compared with unamended groundwater. Community structure was determined using DNA directly extracted from groundwater samples. This DNA was then analyzed by amplified ribosomal DNA restriction analysis. Unique restriction fragment length polymorphisms defined operational taxonomic units that were sequenced to determine phylogeny. DNA sequence data indicated that known TCE-degrading bacteria including relatives of Variovorax and Burkholderia were present in site water. Diversity of the amplified microbial rDNA clone library was lower in phenol-amended communities than in unamended groundwater (i.e., having Shannon–Weaver diversity indices of 2.0 and 2.2, respectively). Microbial activity was higher in phenol-amended ground water as determined by measuring the reduction of 2-(p-iodophenyl)-3(p-nitrophenyl)-5-phenyl tetrazolium chloride. Thus phenol amendments to groundwater correlated with increased TCE mineralization, a decrease in diversity of the amplified microbial rDNA clone library, and increased microbial activity.Key words: community structure, trichloroethylene, degradation, groundwater.

scholarly journals The use of diversity indices for local assessment of marine sediment quality

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shinya Hosokawa ◽  
Kyosuke Momota ◽  
Anthony A. Chariton ◽  
Ryoji Naito ◽  
Yoshiyuki Nakamura
Keyword(s):  
Community Structure ◽  
Sample Size ◽  
Small Sample Size ◽  
Benthic Communities ◽  
Sediment Quality ◽  
Diversity Indices ◽  
Small Sample ◽  
Species Density ◽  
Local Case ◽  
Two Indices

AbstractDiversity indices are commonly used to measure changes in marine benthic communities. However, the reliability (and therefore suitability) of these indices for detecting environmental change is often unclear because of small sample size and the inappropriate choice of communities for analysis. This study explored uncertainties in taxonomic density and two indices of community structure in our target region, Japan, and in two local areas within this region, and explored potential solutions. Our analysis of the Japanese regional dataset showed a decrease in family density and a dominance of a few species as sediment conditions become degraded. Local case studies showed that species density is affected by sediment degradation at sites where multiple communities coexist. However, two indices of community structure could become insensitive because of masking by community variability, and small sample size sometimes caused misleading or inaccurate estimates of these indices. We conclude that species density is a sensitive indicator of change in marine benthic communities, and emphasise that indices of community structure should only be used when the community structure of the target community is distinguishable from other coexisting communities and there is sufficient sample size.

scholarly journals Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis

2016 ◽  
Vol 62 (6) ◽  
pp. 485-491 ◽  
Author(s):  
Samiran Banerjee ◽  
Nabla Kennedy ◽  
Alan E. Richardson ◽  
Keith N. Egger ◽  
Steven D. Siciliano
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Archaeal Community ◽  
Diversity Indices ◽  
High Arctic ◽  
Total Carbon ◽  
Spatial Dependency ◽  
Edaphic Factors ◽  
Total Carbon Content ◽  
Arctic Soils

Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2–5 m scale (P < 0.05), whereas AOA communities were dependent at the ∼1 m scale (P < 0.0001). Soil moisture, pH, and total carbon content were key edaphic factors driving both the ARC and AOA community structure. However, AOA evenness had simultaneous correlations with dissolved organic nitrogen and mineral nitrogen, indicating a possible niche differentiation for AOA in which dry mineral and wet organic soil microsites support different AOA genotypes. Richness, evenness, and diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases.

Diversity and community structure of Ephemeroptera in freshwater stream of Megamalai hills, Tamil Nadu, India

ENTOMON ◽  
2021 ◽  
Vol 46 (4) ◽  
pp. 279-284
Author(s):  
S. Barathy ◽  
T. Sivaruban ◽  
Srinivasan Pandiarajan ◽  
Isack Rajasekaran ◽  
M. Bernath Rosi
Keyword(s):  
Community Structure ◽  
Species Diversity ◽  
Air Temperature ◽  
Tamil Nadu ◽  
Dominant Species ◽  
Diversity Indices ◽  
Low Diversity ◽  
Freshwater Stream ◽  
Species Diversity Indices ◽  
High Diversity

In the study on the diversity and community structure of Ephemeroptera in the freshwater stream of Chinnasuruli falls on Megamalai hills, a total of 523 specimens belonging to thirteen genera and five families were collected in six month periods. Of the five families, Teloganodidae and Leptophlebiidae exhibited high diversity and Caenidae showed low diversity. Choroterpes alagarensis (Leptophlebiidae) is the most dominant species. Diversity indices such as Shannon and Simpson indices showed that diversity was maximum in November and December and it was minimum in August and January. Canonical Correspondence Analysis revealed that rainfall, water flow, turbidity, and air temperature were the major stressors in affecting the Ephemeropteran community structure.

Dynamics of the prokaryotic and eukaryotic microbial community during a cyanobacterial bloom

2021 ◽  
Author(s):  
Yilin Qian ◽  
Kunihiro Okano ◽  
Miwa Kodato ◽  
Michiko Arai ◽  
Takeru Yanagiya ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Negative Correlation ◽  
Aquatic Environment ◽  
Cyanobacterial Bloom ◽  
Cyanobacterial Blooms ◽  
Gene Copy ◽  
Degrading Bacteria ◽  
Freshwater Bodies ◽  
Predator Community

Abstract Toxic cyanobacterial blooms frequently develop in eutrophic freshwater bodies worldwide. Microcystis species produce microcystins (MCs) as a cyanotoxin. Certain bacteria that harbor the mlr gene cluster, especially mlrA, are capable of degrading MCs. However, MCs-degrading bacteria may possess or lack mlr genes (mlr+ and mlr− genotypes, respectively). In this study we investigated the genotype that predominantly contributes to biodegradation and cyanobacterial predator community structure with change in total MCs concentration in an aquatic environment. The two genotypes co-existed but mlr+ predominated, as indicated by the negative correlation between mlrA gene copy abundance and total MCs concentration. At the highest MCs concentrations, predation pressure by Phyllopoda, Copepoda, and Monogononta (rotifers) was reduced; thus, MCs may be toxic to cyanobacterial predators. The results suggest cooperation between MCs-degrading bacteria and predators may reduce Microcystis abundance and MCs concentration.

scholarly journals Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome

2021 ◽  
Vol 22 (21) ◽  
pp. 12050
Author(s):  
Cynthia B. Silveira ◽  
Ana G. Cobián-Güemes ◽  
Carla Uranga ◽  
Jonathon L. Baker ◽  
Anna Edlund ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Lung Function ◽  
Sequence Data ◽  
Anaerobic Bacteria ◽  
Keystone Species ◽  
Clinical Diagnostics ◽  
Epifluorescence Microscopy ◽  
Fermentation Products ◽  
Degrading Bacteria

Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient’s lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient’s strain was resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.

scholarly journals Effect of Farming and Rainfall on the Species Diversity, Population Density and Community Structure of Birds Breeding in the Kalahari Woodland, NE Namibia

Zoodiversity ◽  
2021 ◽  
Vol 55 (6) ◽  
pp. 451-458
Author(s):  
G. Kopij
Keyword(s):  
Community Structure ◽  
Species Diversity ◽  
Bird Species ◽  
Diversity Indices ◽  
Annual Rainfall ◽  
Feeding Guilds ◽  
Line Transect ◽  
Population Densities ◽  
Feeding Guild ◽  
Turtle Dove

The line transect method has been employed to assess species diversity, population densities and community structure of birds breeding in a mosaic of Kalahari Woodland and farmland, NE Namibia. The transect, 4.5 km long, was surveyed in 2014 and 2015. The total annual rainfall in 2014 was much higher than in 2015 (427 mm vs. 262 mm). In total, 40 breeding species in 2014, and 46 in 2015 were recorded. Six species were dominant in 2014 (Cape Turtle Dove, Laughing Dove, Emerald-spotted Dove, Blue Waxbill, and White-browed Scrub Robin) and only three species in 2015 (Cape Turtle Dove and Blue Waxbill and Yellow-fronted Canary). Although the cumulative dominance in 2014 almost doubled that in 2015, the Community Index in both years was almost identical. Also diversity indices and evenness index were very similar in both years compared. Granivorous birds were the most numerous feeding guild. Their contribution was similar in 2014 and 2015 (46.7 % vs. 43.4 %). Two other feeding guilds, insectivores and frugivores, comprised together more than 50 % in both years. The number of bird species and species diversity were not influenced by the differential rainfall. However, contrary to expectations, population densities of most bird species (at least the more numerous ones) were higher in the year with lower than in the year with higher rainfall. The number of species and species diversity was similar in the farmland and in neighbouring Kalahari Woodland in a pristine stage. However, population densities of most species were lower in the farmland than in the pristine woodland.

scholarly journals Flexible Community Structure Correlates with Stable Community Function in Methanogenic Bioreactor Communities Perturbed by Glucose

2000 ◽  
Vol 66 (9) ◽  
pp. 4058-4067 ◽  
Author(s):  
Ana S. Fernandez ◽  
Syed A. Hashsham ◽  
Sherry L. Dollhopf ◽  
Lutgarde Raskin ◽  
Olga Glagoleva ◽  
...  
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Restriction Analysis ◽  
Companion Paper ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Ssu Rrna ◽  
Rdna Genes ◽  
Community Function ◽  
Fermentative Bacteria

ABSTRACT Methanogenic bioreactor communities were used as model ecosystems to evaluate the relationship between functional stability and community structure. Replicated methanogenic bioreactor communities with two different community structures were established. The effect of a substrate loading shock on population dynamics in each microbial community was examined by using morphological analysis, small-subunit (SSU) rRNA oligonucleotide probes, amplified ribosomal DNA (rDNA) restriction analysis (ARDRA), and partial sequencing of SSU rDNA clones. One set of replicated communities, designated the high-spirochete (HS) set, was characterized by good replicability, a high proportion of spiral and short thin rod morphotypes, a dominance of spirochete-related SSU rDNA genes, and a high percentage ofMethanosarcina-related SSU rRNA. The second set of communities, designated the low-spirochete (LS) set, was characterized by incomplete replicability, higher morphotype diversity dominated by cocci, a predominance of Streptococcus-related and deeply branching Spirochaetales-related SSU rDNA genes, and a high percentage of Methanosaeta-related SSU rRNA. In the HS communities, glucose perturbation caused a dramatic shift in the relative abundance of fermentative bacteria, with temporary displacement of spirochete-related ribotypes byEubacterium-related ribotypes, followed by a return to the preperturbation community structure. The LS communities were less perturbed, with Streptococcus-related organisms remaining prevalent after the glucose shock, although changes in the relative abundance of minor members were detected by morphotype analysis. A companion paper demonstrates that the more stable LS communities were less functionally stable than the HS communities (S. A. Hashsham, A. S. Fernandez, S. L. Dollhopf, F. B. Dazzo, R. F. Hickey, J. M. Tiedje, and C. S. Criddle, Appl. Environ. Microbiol. 66:4050–4057, 2000).

scholarly journals Achromobacter buckle infection diagnosed by a 16S rDNA clone library analysis: a case report

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Fumika Hotta ◽  
Hiroshi Eguchi ◽  
Takeshi Naito ◽  
Yoshinori Mitamura ◽  
Kohei Kusujima ◽  
...  
Keyword(s):  
Case Report ◽  
16S Rdna ◽  
Clone Library ◽  
16S Rdna Clone Library ◽  
Clone Library Analysis ◽  
Rdna Clone ◽  
Buckle Infection

Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters

2018 ◽  
Vol 75 (7) ◽  
pp. 918-924 ◽  
Author(s):  
Luanfeng Hou ◽  
Qingping Wu ◽  
Qihui Gu ◽  
Qin Zhou ◽  
Jumei Zhang
Keyword(s):  
Community Structure ◽  
Structure Analysis ◽  
Degrading Bacteria
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