Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members

Genome ◽  
2013 ◽  
Vol 56 (10) ◽  
pp. 599-611 ◽  
Author(s):  
Boonfei Tan ◽  
Xiaoli Dong ◽  
Christoph W. Sensen ◽  
Julia Foght
Keyword(s):  
Microbial Community ◽  
Oil Sands ◽  
Hydrogenase Activity ◽  
Microbial Culture ◽  
Alkane Degradation ◽  
Metabolic Functions ◽  
Anaerobic Hydrocarbon Degradation ◽  
Suitable Reference ◽  
Protein Recruitment ◽  
Paired End Sequencing

A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6–C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic–fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO2 fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Microbial community dynamics of surface water in British Columbia, Canada

2019 ◽  
Author(s):  
Miguel I. Uyaguari-Diaz ◽  
Matthew A. Croxen ◽  
Kirby Cronin ◽  
Zhiyao Luo ◽  
Judith Isaac-Renton ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Community Dynamics ◽  
Fecal Contamination ◽  
Rrna Gene ◽  
Microbial Culture ◽  
Sample Collection ◽  
Fecal Indicator ◽  
E Coli

AbstractTraditional methods for monitoring the microbiological quality of water focus on the detection of fecal indicator bacteria such as Escherichia coli, often tested as a weekly grab sample. To understand the stability of E.coli concentrations over time, we evaluated three approaches to measuring E. coli levels in water: microbial culture using Colilert, quantitative PCR for uidA and next-generation sequencing of the 16S rRNA gene. Two watersheds, one impacted by agricultural and the other by urban activities, were repeatedly sampled over a simultaneous ten-hour period during each of the four seasons. Based on 16S rRNA gene deep sequencing, each watershed showed different microbial community profiles. The bacterial microbiomes varied with season, but less so within each 10-hour sampling period. Enterobacteriaceae comprised only a small fraction (<1%) of the total community. The qPCR assay detected significantly higher quantities of E. coli compared to the Colilert assay and there was also variability in the Colilert measurements compared to Health Canada’s recommendations for recreational water quality. From the 16S data, other bacteria such as Prevotella and Bacteroides showed promise as alternative indicators of fecal contamination. A better understanding of temporal changes in watershed microbiomes will be important in assessing the utility of current biomarkers of fecal contamination, determining the best timing for sample collection, as well as searching for additional microbial indicators of the health of a watershed.

Nitrogen- and sulfur-deposition-altered soil microbial community functions and enzyme activities in a boreal mixedwood forest in western Canada

2013 ◽  
Vol 43 (9) ◽  
pp. 777-784 ◽  
Author(s):  
Ya-Lin Hu ◽  
Kangho Jung ◽  
De-Hui Zeng ◽  
Scott X. Chang
Keyword(s):  
Microbial Community ◽  
Microbial Biomass ◽  
Soil Microbial Community ◽  
Oil Sands ◽  
Soil Microbial Biomass ◽  
Soil Microbial ◽  
C And N ◽  
Boreal Mixedwood Forest ◽  
The Impact ◽  
S Deposition

Chronic nitrogen (N) and (or) sulfur (S) deposition to boreal forests in the Athabasca oil sands region (AOSR) in Alberta, Canada, has been caused by oil sands mining and extraction/upgrading activities. It is important that we understand the response of microbial community function to chronic N and S deposition as microbial populations mediate soil carbon (C) and N cycles and affect ecosystem resilience. To evaluate the impact of N and (or) S deposition on soil microbial community functions, we conducted a simulated N and S deposition experiment in a boreal mixedwood forest with the following four treatments: control (CK), N addition (+N, 30 kg N·ha−1 as NH4NO3), S addition (+S, 30 kg S·ha−1 as NaSO4), and N plus S addition (+NS, 30 kg N·ha−1 + 30 kg S·ha−1), from 2006 to 2010. Nitrogen and (or) S deposition did not change soil organic carbon, total N, dissolved organic C and N, or soil microbial biomass C and N. Soil microbial community-level physiological profiles, however, were strongly affected by 5 years of N and (or) S addition. Soil β-glucosidase activity in the +NS treatment was greater than that in the +S treatment, and S addition decreased soil arylsulfatase; however, urease and dehydrogenase activities were not affected by the simulated N and (or) S deposition. Our data suggested that N and (or) S deposition strongly affected soil microbial community functions and enzymatic activities without changing soil microbial biomass in the studied boreal forest.

scholarly journals Responses of microbial community from tropical pristine coastal soil to crude oil contamination

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1733 ◽  
Author(s):  
Daniel Morais ◽  
Victor Pylro ◽  
Ian M. Clark ◽  
Penny R. Hirsch ◽  
Marcos R. Tótola
Keyword(s):  
Microbial Community ◽  
Crude Oil ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Oceanic Islands ◽  
Oil Contamination ◽  
Target Sequencing ◽  
Metabolic Functions ◽  
Crude Oil Contamination ◽  
Bacteria And Fungi

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg−1), in triplicate. Soils were incubated for 38 days, with CO2measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

scholarly journals Profiling the microbial community structure and functional diversity of a dam-regulated river undergoing gravel bar restoration

2020 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Bin Li ◽  
Tetsuya Sumi ◽  
Yasuhiro Takemon ◽  
Kozo Watanabe
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Beta Diversity ◽  
Environmental Heterogeneity ◽  
Trinity River ◽  
Metabolic Functions ◽  
Gravel Bars ◽  
Gravel Bar ◽  
The Trinity

AbstractBackgroundRiver restoration efforts are expected to influence and change the diversity and functions of microbial communities following the recovery of habitat characteristics in the river ecosystem. The recreation or restoration of gravel bars in the Trinity River in California aims to rehabilitate the environmental heterogeneity downstream of the dam impounded channel. Here, we profiled the community composition, estimated diversity, and annotated putative metabolic functions of the sediment microbial communities to assess whether the construction and restoration of gravel bars in the Trinity River in California enhanced environmental heterogeneity, with the increase in the microbial beta diversity of these in-channel structures against the free-flowing reach of the main channel with comparison to its undisturbed tributaries.ResultsMicrobial community composition of the free-flowing (i.e., no gravel bars) communities were relatively closer regardless of dam influence, whereas the Trinity River gravel bar and tributaries’ gravel bar communities were highly dissimilar. Proteobacteria, Bacteroidetes, and Acidobacteria were the highly abundant sediment microbial phyla on most sites, specifically in the Trinity River gravel bar communities. Putative functional annotation of microbial taxa revealed that chemoheterotrophy and aerobic chemoheterotrophy were the most prevalent microbial processes, with the Trinity River gravel bars having relatively higher representations. The considerably large abundance of heterotrophic taxa implies that gravel bars provide suitable areas for heterotrophic microorganisms with metabolic functions contributing to the net respiration in the river.ConclusionsOur results provide supporting evidence on the positive impact of habitat restoration being conducted in the Trinity River with the non-dam influenced, undisturbed tributaries as the basis of comparison. Gravel bar recreation and restoration contributed to the increased microbial biodiversity through the restoration of environmental heterogeneity at the river scale. We provided valuable insights into the potential microbial processes in the sediment that might be contributing to the biogeochemical processes carried out by the microbial communities in the Trinity River. The significant positive correlation between the functional diversity of the identified microbial taxa and beta diversity suggests that differences in the detected metabolic functions were closely related to dissimilarities in community composition.

scholarly journals Effects of Long-Term Discharge of Acid Mine Drainage from Abandoned Coal Mines on Soil Microorganisms: Microbial Community Structure, Interaction Patterns and Metabolic Functions

2021 ◽  
Author(s):  
Di Chen ◽  
Qiyan Feng ◽  
Haoqian Liang
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Coal Mines ◽  
Interaction Patterns ◽  
Nitrogen Fixing ◽  
Acid Mine ◽  
Metabolic Functions ◽  
Abandoned Coal Mines

Abstract More than twenty abandoned coal mines in the Yudong River basin of Guizhou Province have discharged acid mine drainage (AMD) for a long time. The revelation of microbial community composition, interaction patterns and metabolic functions can contributes to the ecological remediation of AMD pollution. In this study, reference and contaminated soils were collected along the AMD flow path for high-throughput sequencing. Results showed that the long-term AMD pollution promoted the evolution of γ-Proteobacteria, and the acidophilic iron-oxidizing bacteria Ferrovum (relative abundance of 15.50%) and iron-reducing bacteria Metallibacterium (9.87%) belonging to this class became the dominant genera. Co-occurrence analysis revealed that the proportion of positive correlations among bacteria increased from 51.02% (reference soil) to 75.16% (contaminated soil), suggesting that acidic pollution promotes the formation of mutualistic interaction networks of microorganisms. Metabolic function prediction (Tax4Fun) revealed that AMD contamination enhanced the microbial functions such as translation, repair, and biosynthesis of peptidoglycan and lipopolysaccharide etc., which may be an adaptive mechanism for microbial survival in extremely acidic environment. In addition, the acidic pollution promoted the high expression of nitrogen fixing genes in soil, and the discovery of autotrophic nitrogen fixing bacteria such as Ferrovum provided the possibility of bioremediation of AMD pollution.

scholarly journals Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones

2020 ◽  
Vol 17 (2) ◽  
pp. 436 ◽  
Author(s):  
Yongkui Yang ◽  
Longfei Wang ◽  
Feng Xiang ◽  
Lin Zhao ◽  
Zhi Qiao
Keyword(s):  
Wastewater Treatment ◽  
Microbial Community ◽  
Activated Sludge ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Wastewater Sludge ◽  
Community Diversity ◽  
Nitrogen And Phosphorus ◽  
Metabolic Functions

Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs.

Sign in / Sign up

Export Citation Format

Share Document