Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

Suprokash Koner; Jung-Sheng Chen; Bing-Mu Hsu; Chao-Wen Tan; Cheng-Wei Fan; Tsung-Hsien Chen; Bashir Hussain; Viji Nagarajan

doi:10.3390/microorganisms9081789

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

10.21203/rs.3.rs-549787/v1 ◽

2021 ◽

Author(s):

Suprokash Koner ◽

Jung-Sheng Chen ◽

Bing-Mu Hsu ◽

Chao-Wen Tan ◽

Cheng-Wei Fan ◽

...

Keyword(s):

Amino Acids ◽

Microbial Community ◽

Amino Acid ◽

Calcium Carbonate ◽

Energy Metabolism ◽

Carbon Source ◽

16S Rrna ◽

Bacterial Communities ◽

Utilization Rate ◽

Biolog Ecoplate

Abstract Microbially induced calcium carbonate precipitation (MICP), a widespread biochemical process involving heterotopic bacterial communities, generally occurs in organic matter-rich environments. Limestone caves, whose oligotrophic conditions result from the absence of sunlight, are considered an extreme environment. In such environments, bacteria have the potential to form calcium carbonate. In this study, the microbial community diversity and taxonomical structure outside and inside a limestone cave was investigated with their community-level carbon source by fingerprinting and functional metabolic pathway prediction using 16S rRNA amplicon sequencing analysis. The Biolog EcoPlate™ assay revealed that microbes from outside the cave were metabolically highly active, resulting in a rising carbon source utilization rate curve. Conversely, the microbial community within the cave was not very active in consuming the carbon substrates of Biolog EcoPlate™. Although major carbon sources were found to be used by microbial communities both inside and outside the cave, the microbial utilization rate of carbon bacteria inside was much lower than for bacteria outside the cave. The taxonomic classification of microbial diversity using 16S rRNA metagenomic analysis revealed eight predominant bacterial phyla associated with both sampling areas: Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Nitrospirae, Chloroflexi, Gemmatimonadetes, and Cyanobacteria. Among these, Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with external cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with internal cave samples. Functional prediction analysis showed that bacterial communities both inside and outside the cave were functionally involved in the metabolism of carbohydrates, amino acids, other amino acid, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the external cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with internal cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and metagenomically observed metabolic function.

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The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

BioMed Research International ◽

10.1155/2016/3241529 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 18

Author(s):

Wei Song ◽

Lingzhi Li ◽

Hongliang Huang ◽

Keji Jiang ◽

Fengying Zhang ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Communities ◽

Antarctic Fish ◽

16S Rrna Gene Sequencing ◽

Physiological Characteristics ◽

Rrna Gene ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

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Metabolic Changes in Scylla paramamosain During Adaptation to an Acute Decrease in Salinity

Frontiers in Marine Science ◽

10.3389/fmars.2021.734519 ◽

2021 ◽

Vol 8 ◽

Author(s):

Hongzhi Yao ◽

Xing Li ◽

Yuhao Chen ◽

Guoling Liang ◽

Gao Gao ◽

...

Keyword(s):

Amino Acids ◽

Energy Metabolism ◽

Metabolic Pathways ◽

Enrichment Analysis ◽

Metabolic Changes ◽

Scylla Paramamosain ◽

Signal Pathways ◽

Salinity Reduction ◽

Large Production ◽

Production Losses

The mud crab Scylla paramamosain is an important euryhaline mariculture species. However, acute decreases in salinity seriously impact its survival and can result in large production losses. In this study, we evaluated metabolic changes in S. paramamosain exposed to an acute salinity reduction from 23 psu to 3 psu. After the salinity decrease, hemolymph osmolality declined from 726.75 to 642.38 mOsm/kg H2O, which was close to the physiological equilibrium state. Activities of osmolality regulation-related enzymes in the gills, including Na+-K+-ATPase, CA, and V-ATPase all increased. Using LC-MS analysis, we identified 519 metabolites (mainly lipids). Additionally, 13 significant metabolic pathways (P < 0.05) were identified via enrichment analysis, which were mainly related to signal pathways, lipids, and transportation. Our correlation analysis, which combined LC-MS and previous GC-MS data, yielded 28 significant metabolic pathways. Amino acids and energy metabolism accounted for most of these pathways, and lipid metabolism pathways were insignificant. Our results showed that amino acids and energy metabolism were the dominant factors involved in the adaptation of S. paramamosain to acute salinity decrease, and lipid metabolites played a supporting role.

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Carbon utilization phenome of Leptospira interrogans serovar Manilae strain K64

Life Sciences, Medicine and Biomedicine ◽

10.28916/lsmb.5.1.2021.76 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

Ailyn G Manglicmot-Yabes ◽

Sharon Yvette Angelina M. Villanueva ◽

Nina G. Gloriani

Keyword(s):

Amino Acids ◽

Methyl Ester ◽

Malic Acid ◽

Metabolic Pathways ◽

Carbon Sources ◽

The Philippines ◽

Health Concern ◽

Leptospira Interrogans ◽

Carbon Utilization ◽

Leptospira Species

Background: Leptospirosis, an acute febrile disease caused by the pathogenic species of genus Leptospira, is one of the neglected emerging zoonoses that is of global public health concern. The recent genus-wide sequencing of Leptospira isolates led to the need for better understanding of the complex metabolic mechanisms of this organism. However, majority of the published studies on Leptospira metabolism were still the pioneering works of Baseman and Cox in the 60’s and their contemporaries. Knowledge on the carbon sources that supports the growth of a Leptospira species will not only contribute to the limited metabolic studies but will further support the reported genes and metabolic pathways of this organism. Objective: Thus, this study aimed to describe the carbon utilization phenome of Leptospira interrogans serovar Manilae strain K64, one of the dominantly circulating pathogenic Leptospira in the Philippines. Methods: A previously optimized BiologTM Gen III sole carbon utilization phenotype microarray assay protocol for leptospires was adapted. Results: L. interrogans serovar Manilae strain K64 showed utilization of 29 carbon sources belonging to sugars and sugar derivatives, amino acids, methyl ester, carboxylic acid and fatty acids. These were N-acetyl-β-D-mannosamine, N-acetyl-D-galactosamine, N-acetyl neuraminic acid, D-fructose, D-galactose, 3-methyl glucose, D-fucose, L-fucose, L-rhamnose, inosine, D-fructose-6-phosphate, D-gluconic, D-glucuronic acid, glucuronamide, D-saccharic acid, D-aspartic acid, D-serine, L-alanine, L-arginine, L-histidine, L-pyroglutamic acid, L-serine, D-lactic acid methyl ester, citric acid, D-malic acid, L-malic acid, alpha ketoglutaric acid, alpha ketobutyric acid, and acetoacetic acid. Discussion and Conclusion: The carbon sources utilized by L. interrogans serovar Manilae strain K64 agreed well with the identified genes and metabolic pathways among Leptospira species. Moreover, these 29 carbon sources have been previously reported to be associated in the biosynthesis of peptidoglycan, lipopolysaccharide, histidine, sulfur, amino acids, and isoleucine and in other metabolic pathways such as glycolysis, pentose-phosphate, pyruvate and fatty acid in Leptospira spp.

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Differential Impacts of Water Table and Temperature on Bacterial Communities in Pore Water From a Subalpine Peatland, Central China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649981 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wen Tian ◽

Xing Xiang ◽

Hongmei Wang

Keyword(s):

Amino Acids ◽

Bacterial Community ◽

Pore Water ◽

Water Table ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Acid Methyl Ester ◽

Central China ◽

Utilization Rate ◽

Carbon Utilization

The level of water table and temperature are two environmental variables shaping soil bacterial communities, particularly in peatland ecosystems. However, discerning the specific impact of these two factors on bacterial communities in natural ecosystems is challenging. To address this issue, we collected pore water samples across different months (August and November in 2017 and May 2018) with a gradient of water table changes and temperatures at the Dajiuhu peatland, Central China. The samples were analyzed with 16S rRNA high-throughput sequencing and Biolog EcoMicroplates. Bacterial communities varied in the relative abundances of dominant taxa and harbored exclusive indicator operational taxonomic units across the different months. Despite these differences, bacterial communities showed high similarities in carbon utilization, with preferences for esters (pyruvic acid methyl ester, Tween 40, Tween 80, and D-galactonic acid γ-lactone), amino acids (L-arginine and L-threonine), and amines (phenylethylamine and putrescine). However, rates of carbon utilization (as indicated by average well-color development) and metabolic diversity (McIntosh and Shannon index) in May and August were higher than those in November. Redundancy analysis revealed that the seasonal variations in bacterial communities were significantly impacted by the level of the water table, whereas the temperature had a fundamental role in bacterial carbon utilization rate. Co-occurrence analysis identified Sphingomonas, Mucilaginibacter, Novosphingobium, Lacunisphaera, Herminiimonas, and Bradyrhizobium as keystone species, which may involve in the utilization of organic compounds such as amino acids, phenols, and others. Our findings suggest that bacterial community functions were more stable than their compositions in the context of water table changes. These findings significantly expand our current understanding of the variations of bacterial community structures and metabolic functions in peatland ecosystems in the context of global warming and fluctuation of the water table.

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16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates

PeerJ ◽

10.7717/peerj.8417 ◽

2020 ◽

Vol 8 ◽

pp. e8417 ◽

Cited By ~ 2

Author(s):

Qiang Chen ◽

William A. Meyer ◽

Qiuwei Zhang ◽

James F. White

Keyword(s):

Microbial Community ◽

Seed Germination ◽

Bacterial Community ◽

16S Rrna ◽

Seedling Growth ◽

Bacterial Communities ◽

Metagenomic Analysis ◽

High Moisture ◽

Core Microbiome ◽

Dry Climates

Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.

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Functional Diversity of Soil Microbial Communities in Response to the Application of Cefuroxime and/or Antibiotic-Resistant Pseudomonas putida Strain MC1

Sustainability ◽

10.3390/su10103549 ◽

2018 ◽

Vol 10 (10) ◽

pp. 3549 ◽

Cited By ~ 2

Author(s):

Kamila Orlewska ◽

Anna Markowicz ◽

Zofia Piotrowska-Seget ◽

Joanna Smoleń-Dzirba ◽

Mariusz Cycoń

Keyword(s):

Amino Acids ◽

Microbial Community ◽

Pseudomonas Putida ◽

Carboxylic Acids ◽

Functional Diversity ◽

Soil Microbial Community ◽

Carbon Substrate ◽

Antibiotic Resistant ◽

Soil Microbial ◽

Catabolic Activity

Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on this topic, the scope of this study was to assess the functional diversity and catabolic activity of the microbial community in soil treated with XM (1 mg/kg and 10 mg/kg soil) using the community-level physiological profile (CLPP) approach during a 90-day experiment. In addition, the effect of antibiotic-resistant Pseudomonas putida strain MC1 (Ps) was also evaluated. The resistance/resilience concept and multifactorial analysis were used to interpret the data. The results showed that the introduction of XM and/or Ps into the soil caused changes in the catabolic activity and functional diversity of the microbial community. A decrease in the values of the CLPP indices (i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six carbon substrate groups) for the XM-treated soil was generally detected up to 30 days. In turn, at the same time, the activity measured in the Ps-inoculated soil was higher compared to the control soil. A stimulatory effect of XM at 10 mg/kg (XM10) and XM10+Ps on the utilization pattern of each substrate group was found at the following sampling times (days 60 and 90). The AWCD values for the utilization of amines, amino acids, carbohydrates, carboxylic acids, miscellaneous compounds and polymers for these treatments were found to be up to 2.3-, 3.1-, 2.3-, 13-, 3.4- and 3.3-fold higher compared to the values for the nontreated control, respectively. The resistance of the CLPP indices and the AWCD values for the carbon substrate groups were categorized as follows: E > H > R > AWCD and amino acids = carbohydrates > polymers > amines > miscellaneous > carboxylic acids, respectively. The results suggest a low initial resistance of the soil microbial community to XM and/or Ps, and despite the short-term negative effect, the balance of the soil ecosystem may be disturbed.

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Microbial community associated with glucose-induced enhanced biological phosphorus removal

Water Science & Technology ◽

10.2166/wst.2009.545 ◽

2009 ◽

Vol 60 (8) ◽

pp. 2105-2113 ◽

Cited By ~ 6

Author(s):

Guangxue Wu ◽

Ketil B Sørensen ◽

Michael Rodgers ◽

Xinmin Zhan

Keyword(s):

Microbial Community ◽

Carbon Source ◽

Phosphorus Removal ◽

Lactic Acid Production ◽

Carbon Substrate ◽

Molecular Fingerprinting ◽

Enhanced Biological Phosphorus Removal ◽

Biological Phosphorus Removal ◽

Stage 1 ◽

Biological Phosphorus

The microbial community associated with enhanced biological phosphorus removal with glucose as the main carbon source at 11°C was investigated using microscopy and molecular fingerprinting techniques. The study lasted 77 days and comprised two stages—Stage 1 when the mixture of glucose, yeast and dried milk was the organic carbon source and Stage 2 when glucose was the single carbon source. Rhodocyclus-related polyphosphate accumulating organisms, α-Proteobacteria and Bacteroidetes constituted 42% in Stage 1 and 45% in Stage 2, 21% in Stage 1 and 16% in Stage 2, and 10% in Stage 1 and 7% in Stage 2 of the total Bacteria, respectively. The Trichococcus genus from the low GC Gram-positive bacteria was possibly responsible for lactic acid production from glucose. The microbial community was gradually changing throughout the experiment and appeared to stabilize towards the end of the experiment. Periods of suboptimal phosphorus removal could have been caused by competition among different microbial communities for carbon substrate.

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Carbon utilization phenome of Leptospira interrogans serovar Manilae strain K64

Life Sciences, Medicine and Biomedicine ◽

10.28916/lsmb.5.10.2021.76 ◽

2021 ◽

Vol 5 (10) ◽

Author(s):

Ailyn G Manglicmot-Yabes ◽

Sharon Yvette Angelina M. Villanueva ◽

Nina G. Gloriani

Keyword(s):

Amino Acids ◽

Methyl Ester ◽

Malic Acid ◽

Metabolic Pathways ◽

Carbon Sources ◽

The Philippines ◽

Health Concern ◽

Leptospira Interrogans ◽

Carbon Utilization ◽

Leptospira Species

Background: Leptospirosis, an acute febrile disease caused by the pathogenic species of genus Leptospira, is one of the neglected emerging zoonoses that is of global public health concern. The recent genus-wide sequencing of Leptospira isolates led to the need for better understanding of the complex metabolic mechanisms of this organism. However, majority of the published studies on Leptospira metabolism were still the pioneering works of Baseman and Cox in the 60’s and their contemporaries. Knowledge on the carbon sources that supports the growth of a Leptospira species will not only contribute to the limited metabolic studies but will further support the reported genes and metabolic pathways of this organism. Objective: Thus, this study aimed to describe the carbon utilization phenome of Leptospira interrogans serovar Manilae strain K64, one of the dominantly circulating pathogenic Leptospira in the Philippines. Methods: A previously optimized BiologTM Gen III sole carbon utilization phenotype microarray assay protocol for leptospires was adapted. Results: L. interrogans serovar Manilae strain K64 showed utilization of 29 carbon sources belonging to sugars and sugar derivatives, amino acids, methyl ester, carboxylic acid and fatty acids. These were N-acetyl-β-D-mannosamine, N-acetyl-D-galactosamine, N-acetyl neuraminic acid, D-fructose, D-galactose, 3-methyl glucose, D-fucose, L-fucose, L-rhamnose, inosine, D-fructose-6-phosphate, D-gluconic, D-glucuronic acid, glucuronamide, D-saccharic acid, D-aspartic acid, D-serine, L-alanine, L-arginine, L-histidine, L-pyroglutamic acid, L-serine, D-lactic acid methyl ester, citric acid, D-malic acid, L-malic acid, alpha ketoglutaric acid, alpha ketobutyric acid, and acetoacetic acid. Discussion and Conclusion: The carbon sources utilized by L. interrogans serovar Manilae strain K64 agreed well with the identified genes and metabolic pathways among Leptospira species. Moreover, these 29 carbon sources have been previously reported to be associated in the biosynthesis of peptidoglycan, lipopolysaccharide, histidine, sulfur, amino acids, and isoleucine and in other metabolic pathways such as glycolysis, pentose-phosphate, pyruvate and fatty acid in Leptospira spp.

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Comparison of Bacterial Community of Healthy and Erwinia amylovora Infected Apples

The Plant Pathology Journal ◽

10.5423/ppj.nt.04.2021.0062 ◽

2021 ◽

Vol 37 (4) ◽

pp. 396-403

Author(s):

Su-Hyeon Kim ◽

Gyoengjun Cho ◽

Su In Lee ◽

Da-Ran Kim ◽

Youn-Sig Kwak

Keyword(s):

Microbial Community ◽

Bacterial Communities ◽

Metabolic Pathways ◽

Fire Blight ◽

Erwinia Amylovora ◽

Control Strategies ◽

Operational Taxonomic Unit ◽

Fundamental Information ◽

Microbial Community Structures ◽

Blight Disease

Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.

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