1
|
Siriarchawatana P, Harnpicharnchai P, Phithakrotchanakoon C, Kitikhun S, Mayteeworakoon S, Chunhametha S, Eurwilaichitr L, Ingsriswang S. Elucidating potential bioindicators from insights in the diversity and assembly processes of prokaryotic and eukaryotic communities in the Mekong River. ENVIRONMENTAL RESEARCH 2024; 243:117800. [PMID: 38056615 DOI: 10.1016/j.envres.2023.117800] [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: 07/27/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/08/2023]
Abstract
Drivers for spatio-temporal distribution patterns of overall planktonic prokaryotes and eukaryotes in riverine ecosystems are generally not fully understood. This study employed amplicon metabarcoding to investigate the distributions and assembly mechanisms of bacterial and eukaryotic communities in the Mekong River. The prevailing bacteria taxa were found to be Betaproteobacteria, Actinobacteria, and Bacteroidetes, while the dominant eukaryotic organisms were cryptophytes, chlorophytes, and diatoms. The community assemblages were influenced by a combination of stochastic and deterministic processes. Drift (DR) and dispersal limitation (DL), signifying the stochastic mechanism, were the main processes shaping the overall prokaryotic and eukaryotic communities. However, homogeneous selection (HoS), indicating deterministic mechanism, played a major role in the assembly process of core prokaryotic communities, especially in the wet season. In contrast, the core eukaryotic communities including Opisthokonta, Sar, and Chlorophyta were dominated by stochastic processes. The significance of HoS within prokaryotic communities was also found to exhibit a decreasing trend from the upstream sampling sites (Chiang Saen and Chiang Khan, Nong Khai) towards the downstream sites (Mukdahan, and Khong Chiam) of the Mekong River. The environmental gradients resulting from the site-specific variations and the gradual decrease in elevation along the river may have a potential influence on the role of HoS in community assembly. Crucial environmental factors that shape the phylogenetic structure within distinct bins of the core prokaryotic communities including water depth, temperature, chloride, sodium, and sulphate were identified, as inferred by their correlation with the beta Net Relatedness Index (betaNRI) during the wet season. Overall, these findings enhance understanding of the complex mechanisms governing the spatio-temporal dynamics of prokaryotic and eukaryotic communities in the Mekong River. Finally, insights gained from this study could provide information on further use of specific core bacteria as microbial-based bioindicators that are effective for the assessment and conservation of the Mekong River ecosystem.
Collapse
Affiliation(s)
- Paopit Siriarchawatana
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Piyanun Harnpicharnchai
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Chitwadee Phithakrotchanakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supattra Kitikhun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Sermsiri Mayteeworakoon
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Suwanee Chunhametha
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center (ENTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand
| | - Supawadee Ingsriswang
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, Thailand.
| |
Collapse
|
2
|
Noyer M, Bernard M, Verneau O, Palacios C. Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49685-49702. [PMID: 36780079 DOI: 10.1007/s11356-023-25637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/14/2023]
Abstract
Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.
Collapse
Affiliation(s)
- Mégane Noyer
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France
| | - Maria Bernard
- Univ. Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,INRAE, SIGENAE, 78350, Jouy-en-Josas, France
| | - Olivier Verneau
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France.,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.,Unit. for Environmental Sciences and Management, North-West University, Potchefstroom, ZA-2520, South Africa
| | - Carmen Palacios
- Univ. Perpignan Via Domitia, Cefrem, UMR5110, F-66860, Perpignan, France. .,Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110 CNRS-UPVD Université de Perpignan Via Domitia 52 Avenue Paul Alduy 66860, Perpignan Cedex, France.
| |
Collapse
|
3
|
Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review. Int J Mol Sci 2022; 23:ijms23073737. [PMID: 35409097 PMCID: PMC8998989 DOI: 10.3390/ijms23073737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/19/2022] [Accepted: 03/26/2022] [Indexed: 01/19/2023] Open
Abstract
While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.
Collapse
|
4
|
Garcés-Ruiz M, Calonne-Salmon M, Bremhorst V, Declerck S. Diesel fuel differentially affects hyphal healing in Gigaspora sp. and Rhizophagus irregularis. MYCORRHIZA 2021; 31:413-421. [PMID: 33661390 DOI: 10.1007/s00572-021-01026-5] [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: 11/16/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Hydrocarbon pollution is an increasing problem affecting soil ecosystems. However, some microorganisms can cope with these pollutants and even facilitate plant establishment and thus phytoremediation. Within soil, arbuscular mycorrhizal fungi (AMF) have developed several strategies to survive and flourish under adverse conditions. Among these is the hyphal healing mechanism (HHM), a process allowing hyphae to re-establish integrity after physical injury. This mechanism differs among species and genera of AMF. However, whether and to what extent hydrocarbon pollution impacts the HHM is unknown. Here, the HHM was monitored in vitro on two AMF strains, Rhizophagus irregularis MUCL 41833 and Gigaspora sp. MUCL 52331, under increasing concentrations of diesel (1, 2, and 5% v:v). The addition of diesel slowed-down the HHM in both fungi. On Gigaspora sp., this effect was limited and most hyphae were able to heal after injury. Conversely, all steps of healing were severely impaired in R. irregularis. That fungus reconnected the injured hyphae at a much lower frequency than the Gigaspora sp., instead investing its energy to link neighboring hyphae or roots, or developing new branches from uninjured hyphae.
Collapse
Affiliation(s)
- Mónica Garcés-Ruiz
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Croix du Sud 3, 1348 Louvain-la-Neuve, Belgium
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Croix du Sud 3, 1348 Louvain-la-Neuve, Belgium
| | - Vincent Bremhorst
- Statistical Methodology and Computing Service, Université catholique de Louvain, Voie du Roman Pays 20, 1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Croix du Sud 3, 1348 Louvain-la-Neuve, Belgium.
| |
Collapse
|
5
|
Fernandes G, Aparicio VC, Bastos MC, De Gerónimo E, Labanowski J, Prestes OD, Zanella R, Dos Santos DR. Indiscriminate use of glyphosate impregnates river epilithic biofilms in southern Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:1377-1387. [PMID: 30360269 DOI: 10.1016/j.scitotenv.2018.09.292] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Epilithic biofilms are communities of microorganisms composed mainly of microbial cells, extracellular polymeric substances from the metabolism of microorganisms, and inorganic materials. Biofilms are a useful tool to assess the impact of anthropic action on aquatic environments including the presence of pesticide residues such as glyphosate. The present work seeks to monitor the occurrence of glyphosate and AMPA residues in epilithic biofilms occurring in a watershed. For this, epilithic biofilm samples were collected in the Guaporé River watershed in the fall and spring seasons of 2016 at eight points. Physicochemical properties of the water and biofilms were determined. The determination of glyphosate and AMPA was performed using an ultra-high performance liquid chromatograph coupled to a tandem mass spectrometer. The concentrations of glyphosate and AMPA detected in epilithic biofilms vary with the season (from 90 to 305 μg kg-1 for glyphosate and from 50 to 240 μg kg-1 for AMPA, in fall and spring, respectively) and are strongly influenced by the amount of herbicide applications. Protected locations and those with poor access not demonstrate the presence of these contaminants. In the other seven points of the Guaporé River watershed, glyphosate was detected in concentrations ranging from 10 to 305 μg kg-1, and concentrations of AMPA ranged from 50 to 670 μg kg-1. An overview of the contamination in the Guaporé watershed shows that the most affected areas are located in the Marau sub-watershed, which are strongly influenced by the presence of the city of Marau. This confirms the indiscriminate use of glyphosate in the urban area (weed control, domestic gardens and horticulture) and constitutes a problem for human and animal health. The results showed that biofilms can accumulate glyphosate resulting from the contamination of water courses and are sensitive to the sources of pollution and pesticides present in rivers.
Collapse
Affiliation(s)
- Gracieli Fernandes
- Universidade Federal de Santa Maria, Centro de Ciências Rurais, Departamento de Solos, Avenida Roraima, n° 1000, Bairro Camobi CEP 97105-900, Rio Grande do Sul, Brazil.
| | - Virginia Carolina Aparicio
- Instituto Nacional de Tecnología Agropecuaria INTA EEA Balcarce, Ruta Nacional 226, Km 73,5, Balcarce CP 7620, Buenos Aires, Argentina.
| | | | - Eduardo De Gerónimo
- Instituto Nacional de Tecnología Agropecuaria INTA EEA Balcarce, Ruta Nacional 226, Km 73,5, Balcarce CP 7620, Buenos Aires, Argentina.
| | - Jérôme Labanowski
- Université de Poitiers, Institut de Chimie des Milieux et Matériaux de Poitiers, IC2MP, Poitiers, France.
| | - Osmar Damian Prestes
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e Exatas, Departamento de Química, Avenida Roraima, n° 1000, Bairro Camobi CEP 97105-900, Rio Grande do Sul, Brazil.
| | - Renato Zanella
- Universidade Federal de Santa Maria, Centro de Ciências Naturais e Exatas, Departamento de Química, Avenida Roraima, n° 1000, Bairro Camobi CEP 97105-900, Rio Grande do Sul, Brazil.
| | - Danilo Rheinheimer Dos Santos
- Universidade Federal de Santa Maria, Centro de Ciências Rurais, Departamento de Solos, Avenida Roraima, n° 1000, Bairro Camobi CEP 97105-900, Rio Grande do Sul, Brazil
| |
Collapse
|
6
|
Bacterial diversity in fumarole environments of the Paricutín volcano, Michoacán (Mexico). Extremophiles 2017; 21:499-511. [DOI: 10.1007/s00792-017-0920-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/13/2017] [Indexed: 10/20/2022]
|
7
|
Markande AR, Nerurkar AS. Microcosm-based interaction studies between members of two ecophysiological groups of bioemulsifier producer and a hydrocarbon degrader from the Indian intertidal zone. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14462-14471. [PMID: 27068903 DOI: 10.1007/s11356-016-6625-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 04/03/2016] [Indexed: 06/05/2023]
Abstract
Isolates were obtained from intertidal zone site samples from all five western and one eastern coastal states of India and were screened. These ecophysiological groups of aerobic, mesophilic, heterotrophic, sporulating, and bioemulsifier-producing bacteria were from Planococcaceae and Bacillaceae. This is the first report of bioemulsifier production by Sporosarcina spp., Lysinibacillus spp., B. thuringiensis, and B. flexus. In this group, Solibacillus silvestris AM1 was found to produce the highest emulsification activity (62.5 %EI) and the sample that yielded it was used to isolate the ecophysiological group of non-bioemulsifier-producing, hydrocarbon-degrading bacteria (belonging to Chromatiales and Bacillales). These yielded hitherto unreported degrader, Rheinheimera sp. CO6 which was selected for the interaction studies (in a microcosm) with bioemulsifier-producing S. silvestris AM1. The gas chromatographic study of these microcosm experiments revealed increased degradation of benzene, toluene, and xylene (BTX) and the growth of Rheinheimera sp. CO6 in the presence of bioemulsifier produced by S. silvestris AM1. Enhancement of the growth of S. silvestris AM1 in the presence of Rheinheimera sp. CO6 was observed possibly due to reduced toxicity of BTX suggesting mutualistic association between the two. This study elucidates the presence and interaction between enhancers and degraders in a hydrocarbon-contaminated intertidal zone and contributes to the knowledge during application of the two in remediation processes.
Collapse
Affiliation(s)
- A R Markande
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India, 390002.
- C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Maliba Campus, Bardoli, Gujarat, India, 394 350.
| | - A S Nerurkar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India, 390002
| |
Collapse
|
8
|
Faure D, Bonin P, Duran R. Environmental microbiology reveals the Earth secret life. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13573-13576. [PMID: 26162441 DOI: 10.1007/s11356-015-4968-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Denis Faure
- Institut de Biologie Intégrative de la Cellule, CNRS-CEA-Université Paris-Sud, Saclay Plant Sciences, 91198, Gif-sur-Yvette Cedex, France
| | | | | |
Collapse
|