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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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2
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Garrison CE, Pachiadaki MG, Soliman S, Helfrich A, Taylor GT. Microbes and microplastics: Community shifts along an urban coastal contaminant gradient. Environ Microbiol 2024; 26:e16563. [PMID: 38151777 DOI: 10.1111/1462-2920.16563] [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: 08/04/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023]
Abstract
Plastic substrates introduced to the environment during the Anthropocene have introduced new pathways for microbial selection and dispersal. Some plastic-colonising microorganisms have adapted phenotypes for plastic degradation (selection), while the spatial transport (dispersal) potential of plastic colonisers remains controlled by polymer-specific density, hydrography and currents. Plastic-degrading enzyme abundances have recently been correlated with concentrations of plastic debris in open ocean environments, making it critical to better understand colonisation of hydrocarbon degraders with plastic degradation potential in urbanised watersheds where plastic pollution often originates. We found that microbial colonisation by reputed hydrocarbon degraders on microplastics (MPs) correlated with a spatial contaminant gradient (New York City/Long Island waterways), polymer types, temporal scales, microbial domains and putative cell activity (DNA vs. RNA). Hydrocarbon-degrading taxa enriched on polyethylene and polyvinyl chloride substrates relative to other polymers and were more commonly recovered in samples proximal to New York City. These differences in MP colonisation could indicate phenotypic adaptation processes resulting from increased exposure to urban plastic runoff as well as differences in carbon bioavailability across polymer types. Shifts in MP community potential across urban coastal contaminant gradients and polymer types improve our understanding of environmental plastic discharge impacts toward biogeochemical cycling across the global ocean.
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Affiliation(s)
- Cody E Garrison
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | | | | | - Anthony Helfrich
- School of Professional Development, Stony Brook University, Stony Brook, New York, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
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3
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Roswell M, Harrison T, Genung MA. Biodiversity-ecosystem function relationships change in sign and magnitude across the Hill diversity spectrum. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220186. [PMID: 37246374 PMCID: PMC10225862 DOI: 10.1098/rstb.2022.0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/07/2023] [Indexed: 05/30/2023] Open
Abstract
Motivated by accelerating anthropogenic extinctions, decades of biodiversity-ecosystem function (BEF) experiments show that ecosystem function declines with species loss from local communities. Yet, at the local scale, changes in species' total and relative abundances are more common than species loss. The consensus best biodiversity measures are Hill numbers, which use a scaling parameter, ℓ, to emphasize rarer versus more common species. Shifting that emphasis captures distinct, function-relevant biodiversity gradients beyond species richness. Here, we hypothesized that Hill numbers that emphasize rare species more than richness does may distinguish large, complex and presumably higher-functioning assemblages from smaller and simpler ones. In this study, we tested which values of ℓ produce the strongest BEF relationships in community datasets of ecosystem functions provided by wild, free-living organisms. We found that ℓ values that emphasized rare species more than richness does most often correlated most strongly with ecosystem functions. As emphasis shifted to more common species, BEF correlations were often weak and/or negative. We argue that unconventional Hill diversities that shift emphasis towards rarer species may be useful for describing biodiversity change, and that employing a wide spectrum of Hill numbers can clarify mechanisms underlying BEF relationships. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
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Affiliation(s)
- Michael Roswell
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Tina Harrison
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Mark A. Genung
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
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4
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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5
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Jain A, Balmonte JP, Singh R, Bhaskar PV, Krishnan KP. Spatially resolved assembly, connectivity and structure of particle-associated and free-living bacterial communities in a high Arctic fjord. FEMS Microbiol Ecol 2021; 97:fiab139. [PMID: 34626180 PMCID: PMC8536490 DOI: 10.1093/femsec/fiab139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 01/08/2023] Open
Abstract
The assembly processes that underlie the composition and connectivity of free-living (FL) and particle-associated (PA) bacterial communities from surface to deep waters remain little understood. Here, using phylogenetic null modeling, we quantify the relative influence of selective and stochastic mechanisms that assemble FL and PA bacterial communities throughout the water column in a high Arctic fjord. We demonstrate that assembly processes acting on FL and PA bacterial communities are similar in surface waters, but become increasingly distinct in deep waters. As depth increases, the relative influence of homogeneous selection increases for FL but decreases for PA communities. In addition, dispersal limitation and variable selection increase with depth for PA, but not for FL communities, indicating increased residence time of taxa on particles and less frequent decolonization. As a consequence, beta diversity of PA communities is greater in bottom than in surface waters. The limited connectivity between these communities with increasing depth leads to highly distinct FL and PA bacterial communities in bottom waters. Finally, depth-related trends for FL and PA beta diversity and connectivity in this study are consistent with previous observations in the open ocean, suggesting that assembly processes for FL and PA bacterial communities may also be distinct in other aquatic environments.
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Affiliation(s)
- Anand Jain
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - John Paul Balmonte
- Department of Ecology and Genetics, Uppsala University, Uppsala 752 36, Sweden
- HADAL and NordCEE, Department of Biology, University of Southern Denmark, Odense, 5230, Denmark
| | - Richa Singh
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi 221 005, Uttar Pradesh, India
| | - Parli Venkateswaran Bhaskar
- Ocean Science Group, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry, National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco da Gama 403 804, Goa, India
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6
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Baumas CMJ, Le Moigne FAC, Garel M, Bhairy N, Guasco S, Riou V, Armougom F, Grossart HP, Tamburini C. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions. THE ISME JOURNAL 2021; 15:1695-1708. [PMID: 33452475 PMCID: PMC8163737 DOI: 10.1038/s41396-020-00880-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 01/29/2023]
Abstract
The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.
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Affiliation(s)
- Chloé M. J. Baumas
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Frédéric A. C. Le Moigne
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Marc Garel
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Nagib Bhairy
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Sophie Guasco
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Virginie Riou
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Fabrice Armougom
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
| | - Hans-Peter Grossart
- grid.419247.d0000 0001 2108 8097Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany ,grid.11348.3f0000 0001 0942 1117Institute of Biochemistry and Biology, Postdam University, 14469 Potsdam, Germany
| | - Christian Tamburini
- grid.500499.10000 0004 1758 6271Aix-Marseille Université, Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO, UM 110), Marseille, France
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7
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Garrison CE, Field EK. Introducing a "core steel microbiome" and community functional analysis associated with microbially influenced corrosion. FEMS Microbiol Ecol 2021; 97:5998222. [PMID: 33220682 DOI: 10.1093/femsec/fiaa237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms attached to aquatic steel structures play key roles in nutrient cycling and structural degradation processes. Corrosion-causing microbes are often the focus of studies involving microbially influenced corrosion, yet the roles of remaining community members remain unclear. This study characterizes the composition and functional potential of a 'core steel microbiome' across stainless steel types (304 and 316) and historic shipwreck steel along salinity gradients in North Carolina estuaries. We found higher phylogenetic evenness and diversity on steel surfaces compared to sediment, and at lower salinities. The core steel microbiome was composed of heterotrophic generalist taxa, and community composition was most strongly influenced by salinity. Substrate type was a secondary factor becoming more influential at higher salinities. The core steel microbiome included members of Sphingobacteriia, Cytophagia, Anaerolineaceae, Verrucomicrobiaceae, Chitinophagaceae, and Rheinheimera. While salinity differences led to phylogenetic separations across microbial community assemblages, functional genes were conserved across salinity and steel type. Generalist taxa on steel surfaces likely provide functional stability and biofilm protection for the community with limited functional trade-offs compared to surrounding environments. Further, characterization of a core steel microbiome increases the understanding of these complex steel surface microbial communities and their similarities to core microbiomes in other environments.
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Affiliation(s)
- Cody E Garrison
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
| | - Erin K Field
- Department of Biology, East Carolina University, 1000 E 5th St, Greenville, NC 27858, USA
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8
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Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. WATER RESEARCH 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
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Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
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9
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Housekeeping in the Hydrosphere: Microbial Cooking, Cleaning, and Control under Stress. Life (Basel) 2021; 11:life11020152. [PMID: 33671121 PMCID: PMC7922117 DOI: 10.3390/life11020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022] Open
Abstract
Who’s cooking, who’s cleaning, and who’s got the remote control within the waters blanketing Earth? Anatomically tiny, numerically dominant microbes are the crucial “homemakers” of the watery household. Phytoplankton’s culinary abilities enable them to create food by absorbing sunlight to fix carbon and release oxygen, making microbial autotrophs top-chefs in the aquatic kitchen. However, they are not the only bioengineers that balance this complex household. Ubiquitous heterotrophic microbes including prokaryotic bacteria and archaea (both “bacteria” henceforth), eukaryotic protists, and viruses, recycle organic matter and make inorganic nutrients available to primary producers. Grazing protists compete with viruses for bacterial biomass, whereas mixotrophic protists produce new organic matter as well as consume microbial biomass. When viruses press remote-control buttons, by modifying host genomes or lysing them, the outcome can reverberate throughout the microbial community and beyond. Despite recognition of the vital role of microbes in biosphere housekeeping, impacts of anthropogenic stressors and climate change on their biodiversity, evolution, and ecological function remain poorly understood. How trillions of the smallest organisms in Earth’s largest ecosystem respond will be hugely consequential. By making the study of ecology personal, the “housekeeping” perspective can provide better insights into changing ecosystem structure and function at all scales.
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Zhang C, Cao K, Li Y, Zhao J, Peng W, Cao H, Xiao X. Long-term nitrogen fertilization shaped the nifH, nirK, and nosZ gene community patterns in red paddy soil in south China. Can J Microbiol 2020; 67:310-322. [PMID: 33022188 DOI: 10.1139/cjm-2020-0300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To understand the diversities of diazotrophs and denitrifiers in red paddy soil under long-term fertilization conditions, nifH, nirK, and nosZ libraries were constructed by PCR-RFLP. nirK gene diversity proved to be lower than that of nosZ and nifH, and nirK and nosZ genes were more sensitive to different fertilization treatments than the nifH gene was. The 3 libraries were dominated by diverse microbes, including the Alpha, Beta, Gamma, and Delta subclasses of the Proteobacteria. Long-term addition of urea with straw mulch and azophoska increased the abundance of nonsymbiotic diazotrophs, which indicated that nonsymbiotic diazotrophs were responsible for the majority of the nitrogen-fixing ability in paddy soil. In addition, a potential link between nifH and nosZ was found due to the existence of nitrogen fixers, such as Bradyrhizobium and Ralstonia, in the nosZ library. The main chemical factors affecting the 3 genes were identified: pH was the most important factor of the nifH community; the nirK gene was more affected by pH and organic matter; available potassium and the carbon-to-nitrogen ratio significantly influenced the community structure of the nosZ gene.
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Affiliation(s)
- Cunzhi Zhang
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixun Cao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, Anhui 233100, China
| | - Yue Li
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Juan Zhao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wentao Peng
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Cao
- College of Life Sciences/Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xin Xiao
- College of Resource and Environment, Anhui Science and Technology University, Chuzhou, Anhui 233100, China
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11
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Roberts C, Allen R, Bird KE, Cunliffe M. Chytrid fungi shape bacterial communities on model particulate organic matter. Biol Lett 2020; 16:20200368. [PMID: 32991826 PMCID: PMC7532721 DOI: 10.1098/rsbl.2020.0368] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microbial colonization and degradation of particulate organic matter (POM) are important processes that influence the structure and function of aquatic ecosystems. Although POM is readily used by aquatic fungi and bacteria, there is a limited understanding of POM-associated interactions between these taxa, particularly for early-diverging fungal lineages. Using a model ecological system with the chitin-degrading freshwater chytrid fungus Rhizoclosmatium globosum and chitin microbeads, we assessed the impacts of chytrid fungi on POM-associated bacteria. We show that the presence of chytrids on POM alters concomitant bacterial community diversity and structure, including differing responses between chytrid life stages. We propose that chytrids can act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from POM degradation that modify bacterial POM communities. This study suggests that chytrid fungi have complex ecological roles in aquatic POM degradation not previously considered, including the regulation of bacterial colonization, community succession and subsequent biogeochemical potential.
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Affiliation(s)
- Cordelia Roberts
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro Allen
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Kimberley E Bird
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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