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Kumari S, Choudhary G, Anu K, Devi S. Metagenomics insight into Puga geothermal geyser located in Himalayan Geothermal Belt (Trans-Himalayan Plateau) Ladakh, India. Braz J Microbiol 2024:10.1007/s42770-024-01408-9. [PMID: 38874746 DOI: 10.1007/s42770-024-01408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/25/2024] [Indexed: 06/15/2024] Open
Abstract
Puga geothermal geyser and surrounding area, located in the Himalayan Geothermal Belt of the Trans-Himalayan Plateau in Ladakh, India, are very geographically isolated and considered pristine and free of anthropogenic activities. In this study, we have conducted the first metagenomic investigation of the microbes in and around the geyser. The whole genome sequencing analysis showed the presence of a total of 44.8%, 39.7% and 41.4% bacterial phyla in the PugW, PugS, and PugSo samples respectively, 8.6% of archaeal phyla (in all the samples), unclassified (derived from other sequences, PugW: 27.6%, PugS: 27.6%, and PugSo: 15.5%) and unclassified (derived from bacteria, PugW: 12%, PugS: 13.8%, and PugSo: 13.8%). The majority of archaeal sequences were linked to Euryarchaeota (2.84%) while the majority of the bacterial communities that predominated in most geothermal locations were linked to Pseudomonadota (67.14%) and Bacteroidota (12.52%). The abundant bacterial strains at the species level included Dechloromonas aromatica, Acinetobacter baumannii, and Arcobacter butzleri, in all the samples while the most abundant archaeal species were Methanosaeta thermophile, Methanoregula boonei, and Methanosarcina berkeri. Further, this geothermal geyser metagenome has a large number of unique sequences linked to unidentified and unclassified lineages, suggesting a potential source for novel species of microbes and their products. The present study which only examined one of the many geothermal geysers and springs in the Puga geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the geothermal springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Puga geothermal area, which serve as a repository for unidentified microbial lineages.
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Affiliation(s)
- Shalini Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Geetanjli Choudhary
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
| | - Kumari Anu
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sarita Devi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box 06, Himachal Pradesh, Palampur, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Rout AK, Dixit S, Tripathy PS, Rout SS, Parida SN, Parida PK, Sarkar DJ, Kumar Das B, Singh AK, Behera BK. Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134377. [PMID: 38663298 DOI: 10.1016/j.jhazmat.2024.134377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/11/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024]
Abstract
The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.
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Affiliation(s)
- Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Sangita Dixit
- Center for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to Be University), Bhubaneswar 751003, India
| | - Partha Sarathi Tripathy
- Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Sushree Swati Rout
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756089, Odisha, India
| | - Satya Narayan Parida
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India
| | - Ashok Kumar Singh
- Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, 700120 Kolkata, West Bengal, India; Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, Uttar Pradesh, India.
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3
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Qiu Q, Li H, Sun X, Zhang L, Tian K, Chang M, Li S, Zhou D, Huo H. Study on the estradiol degradation gene expression and resistance mechanism of Rhodococcus R-001 under low-temperature stress. CHEMOSPHERE 2024; 358:142146. [PMID: 38677604 DOI: 10.1016/j.chemosphere.2024.142146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Estradiol (E2), an endocrine disruptor, acts by mimicking or interfering with the normal physiological functions of natural hormones within organisms, leading to issues such as endocrine system disruption. Notably, seasonal fluctuations in environmental temperature may influence the degradation speed of estradiol (E2) in the natural environment, intensifying its potential health and ecological risks. Therefore, this study aims to explore how bacteria can degrade E2 under low-temperature conditions, unveiling their resistance mechanisms, with the goal of developing new strategies to mitigate the threat of E2 to health and ecological safety. In this paper, we found that Rhodococcus equi DSSKP-R-001 (R-001) can efficiently degrade E2 at 30 °C and 10 °C. Six genes in R-001 were shown to be involved in E2 degradation by heterologous expression at 30 °C. Among them, 17β-HSD, KstD2, and KstD3, were also involved in E2 degradation at 10 °C; KstD was not previously known to degrade E2. RNA-seq was used to characterize differentially expressed genes (DEGs) to explore the stress response of R-001 to low-temperature environments to elucidate the strain's adaptation mechanism. At the low temperature, R-001 cells changed from a round spherical shape to a long rod or irregular shape with elevated unsaturated fatty acids and were consistent with the corresponding genetic changes. Many differentially expressed genes linked to the cold stress response were observed. R-001 was found to upregulate genes encoding cold shock proteins, fatty acid metabolism proteins, the ABC transport system, DNA damage repair, energy metabolism and transcriptional regulators. In this study, we demonstrated six E2 degradation genes in R-001 and found for the first time that E2 degradation genes have different expression characteristics at 30 °C and 10 °C. Linking R-001 to cold acclimation provides new insights and a mechanistic basis for the simultaneous degradation of E2 under cold stress in Rhodococcus adaptation.
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Affiliation(s)
- Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Han Li
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Lili Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Menghan Chang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Shuaiguo Li
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China.
| | - Dandan Zhou
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China; Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun, 130117, China.
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun City, Jilin Province, China; Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, Northeast Normal University, Changchun, 130117, China.
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Duan Y, Wang T, Zhang P, Zhao X, Jiang J, Ma Y, Zhu X, Fang W. The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis. PLANT, CELL & ENVIRONMENT 2024; 47:1141-1159. [PMID: 38098148 DOI: 10.1111/pce.14784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/15/2023] [Accepted: 12/06/2023] [Indexed: 03/05/2024]
Abstract
Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.
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Affiliation(s)
- Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ting Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Peixi Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinjie Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jie Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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Yadav P, Das J, Sundharam SS, Krishnamurthi S. Analysis of Culturable Bacterial Diversity of Pangong Tso Lake via a 16S rRNA Tag Sequencing Approach. Microorganisms 2024; 12:397. [PMID: 38399801 PMCID: PMC10892101 DOI: 10.3390/microorganisms12020397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 02/25/2024] Open
Abstract
The Pangong Tso lake is a high-altitude freshwater habitat wherein the resident microbes experience unique selective pressures, i.e., high radiation, low nutrient content, desiccation, and temperature extremes. Our study attempts to analyze the diversity of culturable bacteria by applying a high-throughput amplicon sequencing approach based on long read technology to determine the spectrum of bacterial diversity supported by axenic media. The phyla Pseudomonadota, Bacteriodetes, and Actinomycetota were retrieved as the predominant taxa in both water and sediment samples. The genera Hydrogenophaga and Rheinheimera, Pseudomonas, Loktanella, Marinomonas, and Flavobacterium were abundantly present in the sediment and water samples, respectively. Low nutrient conditions supported the growth of taxa within the phyla Bacteriodetes, Actinomycetota, and Cyanobacteria and were biased towards the selection of Pseudomonas, Hydrogenophaga, Bacillus, and Enterococcus spp. Our study recommends that media formulations can be finalized after analyzing culturable diversity through a high-throughput sequencing effort to retrieve maximum species diversity targeting novel/relevant taxa.
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Affiliation(s)
- Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh 160036, India; (P.Y.); (J.D.); (S.S.S.)
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad 201002, India
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6
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Fakhraldeen SA, Al-Haddad S, Habibi N, Alagarsamy S, F. K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf. PLoS One 2023; 18:e0291167. [PMID: 37972047 PMCID: PMC10653540 DOI: 10.1371/journal.pone.0291167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.
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Affiliation(s)
- Saja A. Fakhraldeen
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sakinah Al-Haddad
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Nazima Habibi
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Surendraraj Alagarsamy
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sabeena F. K. Habeebullah
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Abdulmuhsen K. Ali
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Walid M. Al-Zakri
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
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Pardo-Esté C, Leiva SG, Remonsellez F, Castro-Nallar E, Castro-Severyn J, Saavedra CP. Exploring the Influence of Small-Scale Geographical and Seasonal Variations Over the Microbial Diversity in a Poly-extreme Athalosaline Wetland. Curr Microbiol 2023; 80:297. [PMID: 37490160 PMCID: PMC10368551 DOI: 10.1007/s00284-023-03395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/26/2023] [Indexed: 07/26/2023]
Abstract
Microorganisms are the most diverse life form on the planet and are critical for maintaining the geochemical cycles, especially in extreme environments. Bacterial communities are dynamic and respond directly to changes in abiotic conditions; among these communities, poly-extremophiles are particularly sensitive to perturbations due to their high specialization. Salar de Huasco is a high-altitude wetland located on the Chilean Altiplano exhibiting several conditions considered extreme for life, including negative water balance, extreme variations in temperature and pH values, high UV radiation, and the presence of various toxic metal(oids). However, previous reports have revealed a diverse bacterial community that has adapted to these conditions, here, we aimed to determine whether microbial community diversity and composition changed in response to geographical and seasonal variations. We found that there are significant differences in diversity, abundance, and composition in bacterial taxa that could be attributed to local geographical and seasonal variations, which in turn, can be associated with microbial traits. In conclusion, in this poly-extreme environment, small-scale changes can trigger significant changes in the microbial communities that maintain basic biogeochemical cycles. Further in depth analysis of microbial functionality and geo-ecological dynamics are necessary to better understand the relationships between seasonal changes and bacterial communities.
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Affiliation(s)
- Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile
| | - Sergio Guajardo Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto-CEITSAZA, Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Avda. Lircay s/n, Talca, Chile
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile.
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
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Wei L, Zhang Y, Zhang Y, Xu X, Zhu L. Unraveling the response of water quality and microbial community to lake water backflowing in one typical estuary of Lake Taihu, China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:642. [PMID: 37145346 DOI: 10.1007/s10661-023-11190-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/01/2023] [Indexed: 05/06/2023]
Abstract
To investigate the effect of lake water backflowing on the aquatic ecosystem in the estuary, surface water samples in the backflowing and unbackflowing areas were collected from one typical estuary of Lake Taihu, Xitiaoxi River. 16S rRNA sequencing and redundancy analysis were conducted to quantitatively elucidate the correlation between microbial community and water quality parameters. Results indicated lake water backflowing would affect the relative distribution of nitrogen species and increase the concentration of total nitrogen (TN) and nitrate, especially in the outlets of municipal sewage and agricultural drainage. For backflowing areas, more frequent water exchange could lower the seasonal fluctuation of the abundance and diversity of microbial community. RDA results showed crucial water quality parameters that greatly influence bacterial community were total organic carbon (TOC), total dissolved solids (TDS), salinity (SAL), ammonia, nitrate, TN for backflowing areas, and TOC, TDS, SAL, ammonia, TN without nitrate for unbackflowing areas. Verrucomicrobia, Proteobacteria, Microcystis, and Arcobacter were dominant with 27.7%, 15.7%, 30.5%, and 25.7% contribution to the overall water quality in backflowing areas. Chloroflexi, Verrucomicrobia, Flavobacterium, and Nostocaceae were dominant with 25.0%, 18.4%, 22.3%, and 11.4% contribution to the overall water quality in unbackflowing areas. And lake water backflowing might mainly affect the amino acid and carbohydrate metabolism based on the metabolism function prediction. A better understanding of the spatiotemporal changes in water quality parameters and microbial community was obtained from this research to comprehensively assess the effect of lake water backflowing on the estuarine ecosystem.
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Affiliation(s)
- Lecheng Wei
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Yajie Zhang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Ye Zhang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyang Xu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China
- Zhejiang Provincial Engineering Laboratory of Water Pollution Control, 388 Yuhangtang Road, Hangzhou, 310058, China
| | - Liang Zhu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
- Zhejiang Provincial Engineering Laboratory of Water Pollution Control, 388 Yuhangtang Road, Hangzhou, 310058, China.
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Ren Z, Ma K, Jia X, Wang Q, Zhang C, Li X. Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area. MICROBIAL ECOLOGY 2023; 85:904-915. [PMID: 35650293 DOI: 10.1007/s00248-022-02053-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/25/2022] [Indexed: 05/04/2023]
Abstract
Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.
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Affiliation(s)
- Ze Ren
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China.
- School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Kang Ma
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xuan Jia
- College of Education for the Future, Beijing Normal University, Zhuhai, 519087, China
| | - Qing Wang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Cheng Zhang
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Engineering Technology, Beijing Normal University, Zhuhai, 519087, China
| | - Xia Li
- Research and Development Center for Watershed Environmental Eco-Engineering, Advanced Institute of Natural Sciences, Beijing Normal University, 18 Jinfeng Road, Xiangzhou Distract, Zhuhai, 519087, Guangdong, China
- School of Environment, Beijing Normal University, Beijing, 100875, China
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10
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Wei C, Sun D, Yuan W, Li L, Dai C, Chen Z, Zeng X, Wang S, Zhang Y, Jiang S, Wu Z, Liu D, Jiang L, Peng S. Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet. ENVIRONMENTAL RESEARCH 2023; 217:114847. [PMID: 36402183 DOI: 10.1016/j.envres.2022.114847] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms play critical ecological roles in the global biogeochemical cycles. However, extensive information on the microbial communities in Qinghai-Tibet Plateau (QTP), which is the highest plateau in the world, is still lacking, particularly in high elevation locations above 4500 m. Here, we performed a survey of th e soil and water microbial communities in Bamucuo Lake, Tibet, by using shotgun metagenomic methods. In the soil and water samples, we reconstructed 75 almost complete metagenomic assembly genomes, and 74 of the metagenomic assembly genomes from the water sample represented novel species. Proteobacteria and Actinobacteria were found to be the dominant bacterial phyla, while Euryarchaeota was the dominant archaeal phylum. The largest virus, Pandoravirus salinus, was found in the soil microbial community. We concluded that the microorganisms in Bamucuo Lake are most likely to fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-elevation locations with 4555 m, confirming that QTP is a vast and valuable resource pool, in which many microorganisms can be used to develop new bioactive substances and new antibiotics to which pathogenic microorganisms have not yet developed resistance.
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Affiliation(s)
- Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Wenliang Yuan
- College of Mathematics and Information Engineering, Jiaxing University, Jiaxing, 314033, PR China
| | - Lei Li
- Engineering Research Center of AI & Robotics, Ministry of Education, Academy for Engineering & Technology, Fudan University, Shanghai, 200433, PR China
| | - Chaoxu Dai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Zuozhou Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Xiaomin Zeng
- Central South University Xiangya Public Health School, Changsha, 410078, PR China
| | - Shihang Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Yuyang Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China
| | - Dong Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China.
| | - Linhua Jiang
- Engineering Research Center of AI & Robotics, Ministry of Education, Academy for Engineering & Technology, Fudan University, Shanghai, 200433, PR China.
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, 201306, PR China; National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, 201306, China; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, 201306, PR China.
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11
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Kuang B, Xiao R, Hu Y, Wang Y, Zhang L, Wei Z, Bai J, Zhang K, Acuña JJ, Jorquera MA, Pan W. Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake. Front Microbiol 2023; 13:1112669. [PMID: 36713194 PMCID: PMC9874162 DOI: 10.3389/fmicb.2022.1112669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities. Methods The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication. Results Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO4 2- and HS- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways. Discussion Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.
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Affiliation(s)
- Bo Kuang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Rong Xiao
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China,*Correspondence: Rong Xiao, ✉
| | - Yanping Hu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Yaping Wang
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhuoqun Wei
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Kegang Zhang
- Department of Environmental Science and Engineering, North China Electric Power University, Baoding, China
| | - Jacquelinne J. Acuña
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco, Chile
| | - Milko A. Jorquera
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco, Chile
| | - Wenbin Pan
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou, China
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12
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Chen AL, Xu FQ, Su X, Zhang FP, Tian WC, Chen SJ, Gou F, Xing ZL, Xiang JX, Li J, Zhao TT. Water microecology is affected by seasons but not sediments: A spatiotemporal dynamics survey of bacterial community composition in Lake Changshou-The largest artificial lake in southwest China. MARINE POLLUTION BULLETIN 2023; 186:114459. [PMID: 36529016 DOI: 10.1016/j.marpolbul.2022.114459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/09/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
This study aimed to evaluate the correlation between microecology of sediments and water as well as their spatial-temporal variations in Changshou Lake. The results demonstrated that microecology in the lake exhibits spatiotemporal heterogeneity, and microbial diversity of sediments was significantly higher than that of water body. Further, it was found that there was statistically insignificant positive correlation between microecology of sediments and that of water body. PCoA and community structure analysis revealed that the predominant phyla which exhibited significant spatial differences in sediments were Proteobacteria, Actinobacteria and Planctomycetes. While, the distribution of dominant bacteria Actinobacteria and Verrucomicrobia in water body showed significant seasonal differences. Microbial networks analysis indicated that there was a cooperative symbiotic relationship between lake microbial communities. Notably, the same bacterial genus had no significant positive correlation in sediment and water, which suggested that bacteria transport between sediment-water interface does not influence the microecological functions of lake water.
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Affiliation(s)
- Ai-Ling Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Fu-Qing Xu
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xia Su
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Fu-Pan Zhang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Wan-Chao Tian
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Shang-Jie Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Fang Gou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Zhi-Lin Xing
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Jin-Xin Xiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Juan Li
- Chongqing Academy of Chinese Materia medica, Chongqing 400060, China
| | - Tian-Tao Zhao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
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13
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Song D, Huo T, Zhang Z, Cheng L, Wang L, Ming K, Liu H, Li M, Du X. Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192416870. [PMID: 36554758 PMCID: PMC9779402 DOI: 10.3390/ijerph192416870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 05/13/2023]
Abstract
Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.
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Affiliation(s)
- Dan Song
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
| | - Tangbin Huo
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
| | - Zhao Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Lei Cheng
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
| | - Le Wang
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
| | - Kun Ming
- A Reserve Assets Authority, Harbin 150030, China
| | - Hui Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
| | - Mengsha Li
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
- Correspondence: (M.L.); (X.D.)
| | - Xue Du
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
- Heilongjiang River Basin Fisheries Ecology Observation and Research Station of Heilongjiang Province, Harbin 150070, China
- Correspondence: (M.L.); (X.D.)
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14
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Li P, Chen T, An M, Zhang Y, Li Y, Li Y, Wang J. Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122081. [PMID: 36556446 PMCID: PMC9781767 DOI: 10.3390/life12122081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.
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Affiliation(s)
- Peiyang Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Tingyu Chen
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Miao An
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Ying Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Yang Li
- Key Laboratory of Environmental Protection Technology on Water Transport, National Engineering Research Center of Port Hydraulic Construction Technology, Ministry of Transport, Tianjin Research Institute for Water Transport Engineering, Tianjin 300456, China
| | - Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
- Correspondence:
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15
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Rai A, Saha SP, Manvar T, Bhattacharjee A. A shotgun approach to explore the bacterial diversity and a brief insight into the glycoside hydrolases of Samiti lake located in the Eastern Himalayas. J Genet Eng Biotechnol 2022; 20:162. [PMID: 36469176 PMCID: PMC9723087 DOI: 10.1186/s43141-022-00444-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 11/12/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Himalayas have always been an enigma and, being biodiversity hotspots, are considered extremely important from an ecological point of view. Recent advances in studies regarding high-altitude lakes have garnered relevant importance as these habitats could harbor potential psychrophilic and psychrotrophic microbes with bio-prospective applications. Contemplating the above scenario, the present study has been undertaken to understand the diversity and the functional capacities of the microbes thriving in this lake. RESULTS In our present study on Samiti Lake, the abundance of Proteobacteria as the major phylum was seen in both the soil and water samples. Incase of the ABSLW (water) and ABS1 (soil) sample, 148,066 and 239,754 predicted genes, were taken for functional analysis. The KEGG analysis showed that ABSLW and ABS1 had 122,911 and 160,268, genes assigned to KO terms respectively. Whereas in case of COG functional analysis, 104,334 and 130,191 genes were assigned to different COG classes for ABSLW and ABS1 respectively. Further, on studying the glycoside hydrolases, an abundance of GH13, GH2, GH3, GH43, and GH23 in both the soil and water samples were seen. CONCLUSION Our study has provided a comprehensive report about the bacterial diversity and functional capacities of microbes thriving in Samiti Lake. It has also thrown some light on the occurrence of glycoside hydrolases in this region, as they have numerous biotechnological applications in different sectors.
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Affiliation(s)
- Aditi Rai
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
| | - Toral Manvar
- Xcelris Labs Ltd, Ahmedabad, Gujarat 380006 India
| | - Arindam Bhattacharjee
- grid.412222.50000 0001 1188 5260Department of Microbiology, University of North Bengal, P.O. NBU, District Darjeeling, West Bengal, Pin-734013 India
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16
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Singh AK, Kumari M, Sharma N, Rai AK, Singh SP. Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. Curr Genet 2022; 68:565-579. [PMID: 35927361 DOI: 10.1007/s00294-022-01247-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 12/14/2022]
Abstract
Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.
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Affiliation(s)
- Ashutosh Kumar Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Megha Kumari
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India.
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17
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Tsering T, Sillanpää M, Viitala M, Reinikainen SP. Variation of microplastics in the shore sediment of high-altitude lakes of the Indian Himalaya using different pretreatment methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157870. [PMID: 35940264 DOI: 10.1016/j.scitotenv.2022.157870] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Microplastics pollution is a growing environmental concern. However, microplastics studies in high altitude remote lakes are scarce. In this study, microplastics pollution was assessed in the shore sediment of three high altitude lakes in Ladakh of the Indian Himalaya, namely Pangong Lake, Tsomoriri Lake and Tsokar Lake. Sampling of lakes shore sediment was performed in August 2019. Two different pretreatment methods were implemented with sediment samples from same sites, resulting two sets of samples. One set of samples was pretreated utilizing enzymatic degradation together with Fenton reactions. Another set of samples from the same sites were pretreated with 30 % hydrogen peroxide (H2O2) and Fenton reaction. Enzymatically pretreated samples resulted in higher microplastics concentrations than the set of H2O2 pretreated samples, which indicated that microplastics concentrations in sediment samples varies even among samples from the same site and that the pretreatment procedure may impact on the reported microplastics concentrations. Considering both sets of samples, microplastic concentration was 160-1000 MP/kg dw in Pangong Lake, 960-3800 MP/kg dw in Tsomoriri Lake, and 160-1000 MP/kg dw in Tsokar Lake. Blank correction based on the limit of detection and the limit of quantification indicated that microplastics concentrations at some sites of the studied lakes are higher than the limit of detection and the limit of quantification. The findings of this study indicated that the studied lakes in the Indian Himalaya are contaminated with microplastics. In addition, the comparison of microplastics using different pretreatment methods illustrated the importance of harmonization of microplastics studies to enable a reliable comparison among microplastics data. Therefore, this study contributes towards an assessment of microplastics in the high-altitude lakes in Indian Himalaya. The findings attributed towards clearer understanding regarding the need of harmonization of pretreatment methods and demonstrated the importance of reporting complete information in microplastics research.
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Affiliation(s)
- Tenzin Tsering
- LUT School of Engineering Sciences, Lappeenranta-Lahti University of Technology LUT, Sammonkatu 12, 50130 Mikkeli, Finland.
| | - Mika Sillanpää
- Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa
| | - Mirka Viitala
- LUT School of Engineering Sciences, Lappeenranta-Lahti University of Technology LUT, Sammonkatu 12, 50130 Mikkeli, Finland
| | - Satu-Pia Reinikainen
- LUT School of Engineering Sciences, Lappeenranta-Lahti University of Technology LUT, Sammonkatu 12, 50130 Mikkeli, Finland
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Wang D, Tang X, Li R, Wu X. Electrokinetic geosynthetics restrained nitrogen release from sediment to overlying water through porewater drainage. CHEMOSPHERE 2022; 307:135674. [PMID: 35835238 DOI: 10.1016/j.chemosphere.2022.135674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Porewater is the primary carrier of sediment nitrogen and a crucial source of overlying water nitrogen; its separation thus is essential for restraining nitrogen release from sediment to overlying water. We developed a novel device using electrokinetic geosynthetics to drain porewater with nitrogen and restrain nitrogen release. A batch experiment lasted 1120 h (about 47 days) was conducted with 20 cm depth of overlying water under three conditions, i.e., undrained at 0 V/cm voltage gradient (control), drained at 0 V/cm, and drained at 0.5 V/cm. Under the pulsed direct current, once porewater drained, overlying water replenished sediment pore space and supplied porewater. Along with porewater drainage, sediment nitrogen concentration was reduced by 11%-30%, decreasing nitrogen release from sediment to overlying water from 83 mg/m2 in the first 100 h to -95 mg/m2 after about 600 h. Processes such as electroosmosis, electromigration, and redox reaction contributed to the restraint on nitrogen release. This research revealed the potentiality of applying electrokinetic geosynthetics to in-situ restraint on sediment nitrogen release in eutrophic waterbodies such as fishponds.
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Affiliation(s)
- Danyang Wang
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430010, China; Key Lab of Basin Water Resource and Eco-Environmental Science in Hubei Province, Wuhan, 430010, China
| | - Xianqiang Tang
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430010, China; Key Lab of Basin Water Resource and Eco-Environmental Science in Hubei Province, Wuhan, 430010, China.
| | - Rui Li
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430010, China; Key Lab of Basin Water Resource and Eco-Environmental Science in Hubei Province, Wuhan, 430010, China
| | - Xingyi Wu
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430010, China; Key Lab of Basin Water Resource and Eco-Environmental Science in Hubei Province, Wuhan, 430010, China
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Zhu C, Langlois GA, Zhao Y. Effect of Environmental Heterogeneity and Trophic Status in Sampling Strategy on Estimation of Small-Scale Regional Biodiversity of Microorganisms. Microorganisms 2022; 10:2119. [PMID: 36363711 PMCID: PMC9697727 DOI: 10.3390/microorganisms10112119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are diverse and play key roles in lake ecosystems, therefore, a robust estimation of their biodiversity and community structure is crucial for determining their ecological roles in lakes. Conventionally, molecular surveys of microorganisms in lakes are primarily based on equidistant sampling. However, this sampling strategy overlooks the effects of environmental heterogeneity and trophic status in lake ecosystems, which might result in inaccurate biodiversity assessments of microorganisms. Here, we conducted equidistant sampling from 10 sites in two regions with different trophic status within East Lake (Wuhan, China), to verify the reliability of this sampling strategy and assess the influence of environmental heterogeneity and trophic status on this strategy. Rarefaction curves showed that the species richness of microbial communities in the region of the lake with higher eutrophication failed to reach saturation compared with that in lower trophic status. The microbial compositions of samples from the region with higher trophic status differed significantly (P < 0.05) from those in the region with lower trophic status. The result of this pattern may be explained by complex adaptations of lake microorganisms in high eutrophication regions with environmental conditions, where community differentiation can be viewed as adaptations to these environmental selection forces. Therefore, when conducting surveys of microbial biodiversity in a heterogeneous environment, investigators should incorporate intensive sampling to assess the variability in microbial distribution in response to a range of factors in the local microenvironment.
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Affiliation(s)
- Changyu Zhu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Gaytha A. Langlois
- Department of Science and Technology, Bryant University, Smithfield, RI 02917, USA
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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Parida PK, Behera BK, Dehury B, Rout AK, Sarkar DJ, Rai A, Das BK, Mohapatra T. Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:71311-71325. [PMID: 35596862 DOI: 10.1007/s11356-022-20766-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.
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Affiliation(s)
- Pranaya Kumar Parida
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India.
| | - Budheswar Dehury
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Ajaya Kumar Rout
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Dhruba Jyoti Sarkar
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India
| | - Basanta Kumar Das
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Kolkata, 700120, West Bengal, India
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21
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Metagenomics Reveal Microbial Effects of Lotus Root-Fish Co-Culture on Nitrogen Cycling in Aquaculture Pond Sediments. Microorganisms 2022; 10:microorganisms10091740. [PMID: 36144342 PMCID: PMC9501379 DOI: 10.3390/microorganisms10091740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH4+, NO2−, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH4+ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root−fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots.
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Patil MP, Woo HE, Lee IC, Nakashita S, Kim K, Kim JO, Kim K. A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115229. [PMID: 35544980 DOI: 10.1016/j.jenvman.2022.115229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - In-Cheol Lee
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea
| | - Shinya Nakashita
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan
| | - Kyeongmin Kim
- Graduate School of Advanced Science and Engineering, Hiroshima University, Kagamiyama 1-4-1, Higashi-Hiroshima, 739-8527, Hiroshima, Japan; Coastal and Estuarine Sediment Dynamics Group, Port and Airport Research Institute, 3-1-1 Nagase, Yokosuka, 239-0826, Kanagawa, Japan
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan, 48513, Republic of Korea.
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Patil MP, Woo HE, Kim JO, Kim K. Field study on short-term changes in benthic environment and benthic microbial communities using pyrolyzed oyster shells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153891. [PMID: 35182647 DOI: 10.1016/j.scitotenv.2022.153891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
To evaluate the effect of pyrolyzed crushed oyster shells (PCOS) on the remediation of sediments and microbial diversity, a field study was conducted in Buksin Bay, Tongyeong City, Republic of Korea. It was observed that after treatment with PCOS, the concentration of H2S in the sediment of the control site was 287 mg/L. Furthermore, it decreased up to 0 mg/L and remained so until the end of the field study, that is for a period of six months. Moreover, the concentrations of NO2-N + NO3-N, NH4-N, and PO4-P decreased sharply, and the oxidation-reduction potential (ORP) increased after PCOS treatment in pore water and overlying water. Regarding the diversity of microbial communities, the predominance of bacteria from phylum Chlorobi was observed in highly reduced (-410 mV; ORP) sediment, which is well known for the production of H2S. After PCOS treatment, the relative abundance of Chlorobi was sharply suppressed. On the other hand, the predominance of bacteria from the phyla Proteobacteria and Bacteroidetes was observed, and their relative abundance in the PCOS-treated sediment increased throughout the experiment, based on 16S rRNA sequencing. The results demonstrate that the abundance of bacterial communities in the PCOS-treated sediments of Buksin Bay is important for marine ecological functioning, especially for pollutant transformation.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea; School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-ro, Nam-Gu, Busan 48513, Republic of Korea.
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24
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Zhao Y, Min H, Luo K, Zhang R, Chen Q, Chen Z. Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153169. [PMID: 35051480 DOI: 10.1016/j.scitotenv.2022.153169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.
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Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China.
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China.
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Gupta J, Rathour R, Dupont C, Mishra A, Shekhar Thakur I. Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing. BIORESOURCE TECHNOLOGY 2022; 351:126936. [PMID: 35247565 DOI: 10.1016/j.biortech.2022.126936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Most of the discarded waste material paves their way to the utmost common dumping grounds, Landfills. Despite their widespread use, the landfill microbiomes are still not well characterized. Metagenomics approach provides insight into the identification of operational parameters influencing the microbiome composition and their biodegradation competencies. The metagenomic DNA was prepared to explore taxonomical community structure, phylogenetic relationships, and functional profile at the same time. A total of 100,021,052 high-quality filtered reads were acquired with a GC abundance of 62.59%. Taxonomical abundance revealed the dominance of phylum Proteobacteria and genes involved in biomolecules metabolism, aromatic compound degradation, stress tolerance, xenobiotic biodegradation etc. were revealed functionally. The intricate heterogeneous environment of landfill revealed well flourished biogeochemical metabolic profiles including nitrogen metabolism. This is the first study for the generated metagenome of Ghazipur landfill and the obtained results propose that microbial communities in landfill settings are far more intricate than expected. It remain mostly unexplored which demands the usage of multiple platforms for a better understanding.
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Affiliation(s)
- Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Arti Mishra
- Amity University, Noida, Uttar Pradesh 201301, India
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Deng C, Zhao R, Qiu Z, Li B, Zhang T, Guo F, Mu R, Wu Y, Qiao X, Zhang L, Cheng JJ, Ni J, Yu K. Genome-centric metagenomics provides new insights into the microbial community and metabolic potential of landfill leachate microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151635. [PMID: 34774959 DOI: 10.1016/j.scitotenv.2021.151635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Landfills are important sources of microorganisms associated with anaerobic digestion. However, the knowledge on microbiota along with their functional potential in this special habitat are still lacking. In this study, we recovered 1168 non-redundant metagenome-assembled genomes (MAGs) from nine landfill leachate samples collected from eight cities across China, spanning 42 phyla, 73 classes, 114 orders, 189 families, and 267 genera. Totally, 74.1% of 1168 MAGs could not be classified to any known species and 5.9% of these MAGs belonged to microbial dark matter phyla. Two putative novel classes were discovered from landfill leachate samples. The identification of thousands of novel carbohydrate-active enzymes showed similar richness level compared to the cow rumen microbiota. The methylotrophic methanogenic pathway was speculated to contribute significantly to methane production in the landfill leachate because of its co-occurrence with the acetoclastic and hydrogenotrophic methanogenic pathways. The genetic potential of dissimilatory nitrate reduction to ammonium (DNRA) was observed, implying DNRA may play a role in ammonium generation in landfill leachate. These findings implied that landfill leachate might be a valuable microbial resource repository and filled the previous understanding gaps for both methanogenesis and nitrogen cycling in landfill leachate microbiota. Our study provides a comprehensive genomic catalog and substantially provides unprecedented taxonomic and functional profiles of the landfill leachate microbiota.
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Affiliation(s)
- Chunfang Deng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Zhiguang Qiu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.
| | - Tong Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Feng Guo
- School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Rong Mu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yang Wu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xuejiao Qiao
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Liyu Zhang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jay J Cheng
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Biological & Agricultural Engineering Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing 100871, China
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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27
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Zhang T, Zhang X, Li Y, Yang N, Qiao L, Miao Z, Xing J, Zhu D. Study of osmoadaptation mechanisms of halophilic Halomonas alkaliphila XH26 under salt stress by transcriptome and ectoine analysis. Extremophiles 2022; 26:14. [PMID: 35229247 DOI: 10.1007/s00792-022-01256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/04/2022] [Indexed: 11/04/2022]
Abstract
Halophilic bacteria such as the genus Halomonas are promising candidates in diverse industrial, agricultural and biomedical applications. Here, we successfully isolated a halophilic Halomonas alkaliphila strain XH26 from Xiaochaidan Salt Lake, and studied its osmoadaptation strategies using transcriptome and ectoine analysis. Divergent mechanisms were involved in osmoadaptation at different salinities in H. alkaliphila XH26. At moderate salinity (6% NaCl), increased transcriptions of ABC transporters related to iron (III), phosphate, phosphonate, monosaccharide and oligosaccharide import were observed. At high salinity (15% NaCl), transcriptions of flagellum assembly and cell motility were significantly inhibited. The transcriptional levels of ABC transporter genes related to iron (III) and iron3+-hydroxamate import, glycine betaine and putrescine uptake, and cytochrome biogenesis and assembly were significantly up-regulated. Ectoine synthesis and accumulation was significantly increased under salt stress, and the increased transcriptional expressions of ectoine synthesis genes ectB and ectC may play a key role in high salinity induced osmoadaptation. At extreme high salinity (18% NaCl), 5-hydroxyectoine and ectoine worked together to maintain cell survival. Together these results give valuable insights into the osmoadaptation mechanisms of H. alkaliphila XH26, and provide useful information for further engineering this specific strain for increased ectoine synthesis and related applications.
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Affiliation(s)
- Tiantian Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Xin Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Yongzhen Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Ning Yang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Lijuan Qiao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Zengqiang Miao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Jiangwa Xing
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
| | - Derui Zhu
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
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Zhang H, Yang L, Li Y, Wang C, Zhang W, Wang L, Niu L. Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114380. [PMID: 34995945 DOI: 10.1016/j.jenvman.2021.114380] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.
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Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Liu Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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29
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Shen Z, Wang F, Liang Y, Li Y, Liu Q, Liu F. Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake. Lett Appl Microbiol 2021; 75:1093-1102. [PMID: 34890483 DOI: 10.1111/lam.13627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism of how microbes adapted to heavy metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12 989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22·84 and 70·69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.
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Affiliation(s)
- Z Shen
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - F Wang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Y Liang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Y Li
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Q Liu
- HeFei University of Technology, Hefei, China
| | - F Liu
- School of life Sciences, Huaibei Normal University, Huaibei, China
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30
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Reid RP, Oehlert AM, Suosaari EP, Demergasso C, Chong G, Escudero LV, Piggot AM, Lascu I, Palma AT. Electrical conductivity as a driver of biological and geological spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile. Sci Rep 2021; 11:12769. [PMID: 34140571 PMCID: PMC8211675 DOI: 10.1038/s41598-021-92105-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/04/2021] [Indexed: 02/05/2023] Open
Abstract
Reputed to be the driest desert in the world, the Atacama Desert in the Central Andes of Northern Chile is an extreme environment with high UV radiation, wide temperature variation, and minimum precipitation. Scarce lagoons associated with salt flats (salars) in this desert are the surface expression of shallow groundwater; these ponds serve as refugia for life and often host microbial communities associated with evaporitic mineral deposition. Results based on multidisciplinary field campaigns and associated laboratory examination of samples collected from the Puquios of the Salar de Llamara in the Atacama Desert during austral summer provide unprecedented detail regarding the spatial heterogeneity of physical, chemical, and biological characteristics of these salar environments. Four main lagoons ('Puquios') and more than 400 smaller ponds occur within an area less than 5 km2, and are characterized by high variability in electrical conductivity, benthic and planktonic biota, microbiota, lagoon bottom type, and style of mineral deposition. Results suggest that electrical conductivity is a driving force of system heterogeneity. Such spatial heterogeneity within the Puquios is likely to be expanded with temporal observations incorporating expected seasonal changes in electrical conductivity. The complexity of these Andean ecosystems may be key to their ability to persist in extreme environments at the edge of habitability.
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Affiliation(s)
- R P Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA.
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA.
| | - A M Oehlert
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
| | - E P Suosaari
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - C Demergasso
- Centro de Biotecnología , Universidad Católica del Norte, Antofagasta, Chile
| | - G Chong
- Departamento de Ciencias Geológicas , Universidad Católica del Norte, Antofagasta, Chile
| | - L V Escudero
- Centro de Biotecnología , Universidad Católica del Norte, Antofagasta, Chile
| | - A M Piggot
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
- AP Research Inc., Miami, FL, 33157, USA
| | - I Lascu
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - A T Palma
- FisioAqua, Las Condes , 7550024, Santiago, Chile
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31
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Martínez JM, Escudero C, Rodríguez N, Rubin S, Amils R. Subsurface and surface halophile communities of the chaotropic Salar de Uyuni. Environ Microbiol 2021; 23:3987-4001. [PMID: 33511754 DOI: 10.1111/1462-2920.15411] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 01/04/2023]
Abstract
Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl2 , LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.
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Affiliation(s)
- José M Martínez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSIC-UAM), Cantoblanco, Madrid, 28049, Spain
| | - Cristina Escudero
- Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Sergio Rubin
- Université Catholique de Louvain, Earth and Life Institute, Georges Lamaitre Center for Earth and Climate Research, Gante, Belgium.,Centro Nacional de Investigaciones Biotecnológicas, CNIB, Cochabamba, Bolivia
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSIC-UAM), Cantoblanco, Madrid, 28049, Spain.,Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
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Rathour R, Medhi K, Gupta J, Thakur IS. Integrated approach of whole-genome analysis, toxicological evaluation and life cycle assessment for pyrene biodegradation by a psychrophilic strain, Shewanella sp. ISTPL2. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 269:116176. [PMID: 33307397 DOI: 10.1016/j.envpol.2020.116176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) such as pyrene are universal contaminants existing in the environment which have known cancer-causing and mutagenic characteristics. A psychrophilic bacterial strain Shewanella sp. ISTPL2 was isolated from the sediment sample collected from the Pangong lake, Jammu & Kashmir, India. In our previous study, the pyrene degradation potential of the ISTPL2 strain was studied in both mineral salt media as well as in soil artificially spiked with different concentrations of pyrene. Whole-genome sequencing of ISTPL2 strain in the current study highlighted the key genes of pyrene metabolism, including alcohol dehydrogenase and ring hydroxylating dioxygenase alpha-subunit. Pyrene cytotoxicity was evaluated on HepG2, a human hepato-carcinoma cell line. The cytotoxicity of the organic extract decreased with the increasing duration of bacterial treatment. To develop a more sustainable biodegradation approach, the potential impacts were evaluated for human health and ecosystem using life-cycle assessment (LCA) following the ReCiPe methodology for the considered PAH. The results implemented that global warming potential (GWP) had the highest impact, whereas both ecotoxicity and human toxicity had least from this study.
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Affiliation(s)
- Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Kristina Medhi
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India; Central Pollution Control Board (CPCB), Regional Directorate (North), PICUP Bhawan, Lucknow, Uttar Pradesh, 226010, India.
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, Delhi, 110067, India.
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33
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Production and characterization of psychrophilic α-amylase from a psychrophilic bacterium, Shewanella sp. ISTPL2. ACTA ACUST UNITED AC 2020. [DOI: 10.1515/amylase-2020-0001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractA psychrophilic and halophilic bacterial isolate, Shewanella sp. ISTPL2, procured from the pristine Pangong Lake, Ladakh, Jammu and Kashmir, India, was used for the production and characterization of the psychrophilic and alkalophilic α-amylase enzyme. The α-amylase is a critical enzyme that catalyses the hydrolysis of α-1,4-glycosidic bonds of starch molecules and is predominately utilized in biotechnological applications. The highest enzyme activity of partially purified extracellular α-amylase was 10,064.20 U/mL after 12 h of incubation in a shake flask at pH 6.9 and 10 °C. Moreover, the maximum intracellular α-amylase enzyme activity (259.62 U/mL) was also observed at 6 h of incubation. The extracellular α-amylase was refined to the homogeneity with the specific enzyme activity of 36,690.47 U/mg protein corresponding to 6.87-fold purification. The optimized pH and temperature for the α-amylase were found to be pH 8 and 4 °C, respectively, suggesting its stability at alkaline conditions and low or higher temperatures. The amylase activity was highly activated by Cu2+, Fe2+ and Ca2+, while inhibited by Cd2+, Co2+ and Na2+. As per our knowledge, the current study reports the highest activity of a psychrophilic α-amylase enzyme providing prominent biotechnological potential.
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Xing BS, Han Y, Wang XC, Cao S, Wen J, Zhang K. Acclimatization of anaerobic sludge with cow manure and realization of high-rate food waste digestion for biogas production. BIORESOURCE TECHNOLOGY 2020; 315:123830. [PMID: 32688256 DOI: 10.1016/j.biortech.2020.123830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Long-term acclimatization of anaerobic sludge was conducted by operating a mesophilic continuously stirred anaerobic reactor (CSTR) with continuous feeding of food wastes (FW) and cow manure (CM). During the long-term acclimatization, continued increase of enzyme activity was revealed, while the microbial structure tended stable as shown by the Shannon index and microbial community. By biomethane potential analysis, the acclimated sludge had a methane yield about 13 times higher than the initial anaerobic sludge. The acclimated sludge was subsequently used for FW digestion with stepwise organic loading rate increase without CM addition. The functional phyla of Bacteroidetes and Proteobacteria, which originated from CM but not very abundant, were significantly enriched not only during sludge acclimatization with CM addition but also in the process of FW digestion without CM addition. A microbe coexistence network was proposed to support an explanation of the metabolic pathways of FW digestion using the acclimated sludge.
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Affiliation(s)
- Bao-Shan Xing
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China
| | - Yule Han
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China
| | - Xiaochang C Wang
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China.
| | - Sifan Cao
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China
| | - Junwei Wen
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China
| | - Kaidi Zhang
- International Science and Technology Cooperation Center for Urban Alternative Water Resources Development, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Engineering Technology Research Center for Wastewater Treatment and Reuse, Shaanxi, China; Key Laboratory of Environmental Engineering, Shaanxi, China; Xi'an University of Architecture and Technology, No., 13 Yanta Road, Xi'an 710055, China
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Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta. Microorganisms 2020; 8:microorganisms8081181. [PMID: 32756460 PMCID: PMC7464526 DOI: 10.3390/microorganisms8081181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/23/2022] Open
Abstract
Due to the low incidence of precipitation attributed to climate change, many high-altitude Andean lakes (HAALs) and lagoons distributed along the central Andes in South America may soon disappear. This includes La Brava–La Punta, a brackish lake system located south of the Salar de Atacama within a hyper-arid and halophytic biome in the Atacama Desert. Variations in the physicochemical parameters of the water column can induce changes in microbial community composition, which we aimed to determine. Sixteen sampling points across La Brava–La Punta were studied to assess the influence of water physicochemical properties on the aquatic microbial community, determined via 16S rRNA gene analysis. Parameters such as pH and the concentrations of silica, magnesium, calcium, salinity, and dissolved oxygen showed a more homogenous pattern in La Punta samples, whereas those from La Brava had greater variability; pH and total silica were significantly different between La Brava and La Punta. The predominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The genera Psychroflexus (36.85%), Thiomicrospira (12.48%), and Pseudomonas (7.81%) were more abundant in La Brava, while Pseudospirillum (20.73%) and Roseovarius (17.20%) were more abundant in La Punta. Among the parameters, pH was the only statistically significant factor influencing the diversity within La Brava lake. These results complement the known microbial diversity and composition in the HAALs of the Atacama Desert.
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36
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Thakur IS, Roy D. Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases. Int J Mol Sci 2020; 21:ijms21144879. [PMID: 32664313 PMCID: PMC7402316 DOI: 10.3390/ijms21144879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/05/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Most of environment-related diseases often result from multiple exposures of abiotic and/or biotic stressors across various life stages. The application of environmental DNA/RNA (eDNA/eRNA) to advance ecological understanding has been very successfully used. However, the eminent extension of eDNA/eRNA-based approaches to estimate human exposure to biotic and/or abiotic environmental stressors to understand the environmental causes of chronic diseases has yet to start. Here, we introduce the potential of eDNA/eRNA for bio-monitoring of human exposome and health effects in the real environmental or occupational settings. This review is the first of its kind to discuss how eDNA/eRNA-based approaches can be applied for assessing the human exposome. eDNA-based exposome assessment is expected to rely on our ability to capture the genome- and epigenome-wide signatures left behind by individuals in the indoor and outdoor physical spaces through shedding, excreting, etc. Records of eDNA/eRNA exposome may reflect the early appearance, persistence, and presence of biotic and/or abiotic-exposure-mediated modifications in these nucleic acid molecules. Functional genome- and epigenome-wide mapping of eDNA offer great promise to help elucidate the human exposome. Assessment of longitudinal exposure to physical, biological, and chemical agents present in the environment through eDNA/eRNA may enable the building of an integrative causal dynamic stochastic model to estimate environmental causes of human health deficits. This model is expected to incorporate key biological pathways and gene networks linking individuals, their geographic locations, and random multi-hits of environmental factors. Development and validation of monitoring of eDNA/eRNA exposome should seriously be considered to introduce into safety and risk assessment and as surrogates of chronic exposure to environmental stressors. Here we highlight that eDNA/eRNA reflecting longitudinal exposure of both biotic and abiotic environmental stressors may serve as records of human exposome and discuss its application as molecular tools for understanding the toxicogenomics basis of environment-related health deficits.
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Affiliation(s)
- Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Correspondence: (I.S.T.); (D.R.); Tel.: +91-2670-4321 (I.S.T.); +1-30-5348-1694 (D.R.)
| | - Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
- Correspondence: (I.S.T.); (D.R.); Tel.: +91-2670-4321 (I.S.T.); +1-30-5348-1694 (D.R.)
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