Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

Koo, Hyunmin; Mojib, Nazia; Hakim, Joseph A.; Hawes, Ian; Tanabe, Yukiko; Andersen, Dale T.; Bej, Asim K.

doi:10.3389/fmicb.2017.01347

Cited by 51 publications

(47 citation statements)

References 111 publications

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“…To gain more insights into the effects of the inundated conditions on microbial functions, we calculated the relative abundance of potential functional genes related to metabolism pathways at level-1, level-2, and level-3 in the emerged and inundated areas. According to the previous studies [58][59][60] , the low NSTI mean values (0.09 + 0.02) indicated high accuracy of the predicted potential metabolic functions in our study. In general, the functional genes' composition is strongly correlated with taxonomic composition in freshwater ecosystems 2,3,61-64 .…”

Section: Discussionsupporting

confidence: 79%

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Liu

Ren

et al. 2020

Sci Rep

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Water level fluctuations are an inherent feature regulating the ecological structures and functions of lakes. It is vital to understand the effects of water level fluctuations on bacterial communities and metabolic characteristics in freshwater lakes in a changing world. However, information on the microbial community structure and functional properties in permanently and seasonally flooded areas are lacking. Poyang Lake is a typical seasonal lake linked to the Yangtze River and is significantly affected by water level fluctuations. Bottom water was collected from 12 sampling sites: seven inundated for the whole year (inundated areas) and five drained during the dry season (emerged areas). High-throughput 16S rRNA gene sequencing was used to identify the bacterial communities. The results showed that the taxonomic structure and potential functions of the bacterial communities were significantly different between the inundated and emerged areas. Cyanobacteria was dominant in both areas, but the relative abundance of Cyanobacteria was much higher in the emerged areas than in the inundated areas. Bacterial communities were taxonomically sensitive in the inundated areas and functionally sensitive in the emerged areas. Nitrogen, phosphorus, and dissolved organic carbon concentrations and their ratios, as well as dissolved oxygen, played important roles in promoting the bacterial taxonomic and functional compositional patterns in both areas. According to the metabolic predictions based on 16S rRNA gene sequences, the relative abundance of functional genes related to assimilatory nitrate reduction in the emerged areas was higher than in the inundated areas, and the relative abundance of functional genes related to dissimilatory nitrate reduction in the inundated areas was higher. These differences might have been caused by the nitrogen differences between the permanently and seasonally flooded areas caused by intra-annual water level fluctuations. The relative abundance of functional genes associated with denitrification was not significantly different in the inundated and emerged areas. This study improved our knowledge of bacterial community structure and nitrogen metabolic processes in permanently and seasonally flooded areas caused by water level fluctuations in a seasonal lake.Microbial assemblages are fundamental components of aquatic ecosystems and play important roles in driving global energy fluxes and biogeochemical cycling 1 . Microbial communities have high species diversity and genetic diversity 2-5 , which make them sensitive to environmental perturbations 6,7 . The relative balance of external nutrient loading influences microbial functional genes and associated metabolic processes in lake ecosystems 8 . Understanding the taxonomic and functional compositions of microbial communities is essential to elucidating the responses of natural bacterial communities to environmental perturbations, such as hydrological fluctuations and nutrient pollution 9-11 . Poyang Lake (PYL) is a seasonal lake characterized by ...

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Section: Discussionsupporting

confidence: 79%

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Liu

Ren

et al. 2020

Sci Rep

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“…Recently, PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states) has been used to predict the functional characteristics of the bacterial community based on the 16s rRNA homology and conserved feature of functional contribution [22][23][24][25]. This cost-effective bioinformatics tool can use only a few hundred sequences to grasp most of the variations in gene content.…”

Section: Introductionmentioning

confidence: 99%

Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Alami

Xue

et al. 2020

Diversity

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Soil microorganisms are critical factors of plant productivity in terrestrial ecosystems. Coptis chinensis Franch is one of the most important medicinal plants in China. Soil types and cropping systems influence the diversity and composition of the rhizospheric microbial communities. In the current study, we provide detailed information regarding the diversity and composition of the rhizospheric bacterial communities of the C. chinensis plants in continuously cropped fields and fallow fields in two seasons (i.e., winter and summer) using next-generation sequencing. The alpha diversity was higher in the five-year cultivated C. chinensis field (CyS5) and lower in fallow fields (NCS). Significant differences analysis confirmed more biomarkers in the cultivated field soil than in fallow fields. Additionally, the principal coordinate analysis (PcoA) of the beta diversity indices revealed that samples associated with the cultivated fields and fallow fields in different seasons were separated. Besides, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Gemmatimonadetes were the top bacterial phyla. Among these phyla, Proteobacteria were found predominantly and showed a decreasing trend with the continuous cropping of C. chinensis. A phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the abundance of C and N functional genes had a significant difference between the soil samples from cultivated (CyS1, CyS3, and CyS5) and fallow (NCS) fields in two seasons (winter and summer). The principal coordinate analysis (PCoA) based on UniFrac distances (i.e., unweighted and weighted) revealed the variations in bacterial community structures in the soil samples. This study could provide a reference for solving the increasingly severe cropping obstacles and promote the sustainable development of the C. chinensis industry.

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“…PICRUSt well predicted the functional profiling of microbial communities using 16S rRNA sequencing data . The predicted functions affiliated with Amino Acid Metabolism, Carbohydrate Metabolism and Membrane Transport should be common properties of bacterial communities . The metabolic activities related to Xenobiotics Biodegradation and Metabolism could be important for the removal of nitrogen‐containing organic pollutants, and the higher abundance of these functional genes in group C suggested that phenol stimulation could probably enhance the capacity of a bacterial community for xenobiotics removal.…”

Section: Discussionmentioning

confidence: 89%

“…32 The predicted functions affiliated with Amino Acid Metabolism, Carbohydrate Metabolism and Membrane Transport should be common properties of bacterial communities. 33 The metabolic activities related to Xenobiotics Biodegradation and Metabolism could be important for the removal of nitrogen-containing organic pollutants, and the higher abundance of these functional genes in group C suggested that phenol stimulation could probably enhance the capacity of a bacterial community for xenobiotics removal. For both communities, the most prevalent predicted functions were Aminobenzoate Degradation and Benzoate Degradation, which participated in downstream metabolism of nitrogen-containing organic pollutants.…”

Section: Discussionmentioning

confidence: 99%

Bioremediation of nitrogen‐containing organic pollutants using phenol‐stimulated activated sludge: performance and microbial community analysis

Zhang

You

et al. 2018

J of Chemical Tech & Biotech

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BACKGROUND Coking wastewater generally contains high levels of phenolics and nitrogen‐containing organic pollutants, thus seeking an appropriate wastewater treatment strategy is necessary. In this study, the triplicate phenol‐stimulated activated sludges (group C) were constructed for aerobic treatment of nitrogen‐containing organic pollutants (indole, pyridine and quinoline), and glucose‐stimulated sludges (group B) were used as control. RESULTS Both groups maintained high efficiency (>90%) for removal of nitrogen‐containing organic pollutants after long‐term operation (90 days). Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that alpha diversity decreased after receiving nitrogen‐containing pollutants. Glucose exerted protective effects on sludge microbes, but phenol‐stimulated microbial consortia showed greater stability when without supplementation of stimulated substrates. Canonical correspondence analysis and Mantel tests indicated that the microbial community structure was significantly associated with indole and quinoline (P < 0.05). Among the dominant genera, Comamonas was the core genus in both groups for pollutants removal, while Thauera and Sphingomonas should be key functional taxa in glucose‐stimulated sludges, with Pseudoxanthomonas, Brevundimonas and Shinella in phenol‐stimulated sludges. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis suggested that the important functional metabolic capabilities should be those related to Cytochrome P450 enzymes and naphthalene degradation, which were significantly correlated with the nitrogen‐containing organic pollutants (P < 0.05). CONCLUSION The results indicated that phenol‐stimulated microbial consortia could be used for efficient removal of nitrogen‐containing organic pollutants, and therefore could have potential for the bioremediation of coking wastewater. © 2018 Society of Chemical Industry

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Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

Cited by 51 publications

References 111 publications

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake

Structure, Diversity, and Composition of Bacterial Communities in Rhizospheric Soil of Coptis chinensis Franch under Continuously Cropped Fields

Bioremediation of nitrogen‐containing organic pollutants using phenol‐stimulated activated sludge: performance and microbial community analysis

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