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Yuan Z, Zeng Z, Liu F. Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve. Sci Rep 2023; 13:17127. [PMID: 37816825 PMCID: PMC10564911 DOI: 10.1038/s41598-023-44447-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/08/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.
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Affiliation(s)
- Zongsheng Yuan
- College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian, China
| | - Zhihao Zeng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Fang Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
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2
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Keck F, Brantschen J, Altermatt F. A combination of machine-learning and eDNA reveals the genetic signature of environmental change at the landscape levels. Mol Ecol 2023; 32:4791-4800. [PMID: 37436405 DOI: 10.1111/mec.17073] [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: 04/17/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
The current advances of environmental DNA (eDNA) bring profound changes to ecological monitoring and provide unique insights on the biological diversity of ecosystems. The very nature of eDNA data is challenging yet also revolutionizing how biological monitoring information is analysed. In particular, new metrics and approaches should take full advantage of the extent and detail of molecular data produced by genetic methods. In this perspective, machine learning algorithms are particularly promising as they can capture complex relationships between the multiple environmental pressures and the diversity of biological communities. We investigated the potential of a new generation of biomonitoring tools that implement machine-learning techniques to fully exploit eDNA datasets. We trained a machine learning model to discriminate between reference and impacted communities of freshwater macroinvertebrates and assessed its performances using a large eDNA dataset collected at 64 standard federal monitoring sites across Switzerland. We show that a model trained on eDNA is significantly better than a naive model and performs similarly to a model trained on traditional data. Our proof-of-concept shows that such a combination of eDNA and machine learning approaches has the potential to complement or even replace traditional environmental monitoring, and could be scaled along temporal or spatial dimensions.
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Affiliation(s)
- François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, Faculty of Science, University of Zurich, Zurich, Switzerland
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3
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Hilderbrand RH, Bambakidis T, Crump BC. The Roles of Microbes in Stream Restorations. MICROBIAL ECOLOGY 2023; 85:853-861. [PMID: 36695828 DOI: 10.1007/s00248-023-02179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/18/2023] [Indexed: 05/04/2023]
Abstract
The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.
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Affiliation(s)
- Robert H Hilderbrand
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA.
| | - Ted Bambakidis
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
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4
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Diamant ES, Boyd S, Lozano-Huntelman NA, Enriquez V, Kim AR, Savage VM, Yeh PJ. Meta-analysis of three-stressor combinations on population-level fitness reveal substantial higher-order interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161163. [PMID: 36572303 DOI: 10.1016/j.scitotenv.2022.161163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Although natural populations are typically subjected to multiple stressors, most past research has focused on single-stressor and two-stressor interactions, with little attention paid to higher-order interactions among three or more stressors. However, higher-order interactions increasingly appear to be widespread. Consequently, we used a recently introduced and improved framework to re-analyze higher-order ecological interactions. We conducted a literature review of the last 100 years (1920-2020) and reanalyzed 142 ecological three-stressor interactions on species' populations from 38 published papers; the vast majority of these studies were from the past 10 years. We found that 95.8 % (n = 136) of the three-stressor combinations had either not been categorized before or resulted in different interactions than previously reported. We also found substantial levels of emergent properties-interactions that are not due to strong pairwise interactions within the combination but rather uniquely due to all three stressors being combined. Calculating net interactions-the overall accounting for all possible interactions within a combination including the emergent and all pairwise interactions-we found that the most prevalent interaction type is antagonism, corresponding to a smaller than expected effect based on single stressor effects. In contrast, for emergent interactions, the most prevalent interaction type is synergistic, resulting in a larger than expected effect based on single stressor effects. Additionally, we found that hidden suppressive interactions-where a pairwise interaction is suppressed by a third stressor-are found in the majority of combinations (74 %). Collectively, understanding multiple stressor interactions through applying an appropriate framework is crucial for answering fundamental questions in ecology and has implications for conservation biology and population management. Crucially, identifying emergent properties can reveal hidden suppressive interactions that could be particularly important for the ecological management of at-risk populations.
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Affiliation(s)
- Eleanor S Diamant
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Sada Boyd
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | | | - Vivien Enriquez
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Alexis R Kim
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Van M Savage
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA; Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA; Santa Fe Institute, Santa Fe, NM, USA
| | - Pamela J Yeh
- Ecology and Evolutionary Biology, University of California, Los Angeles, USA; Santa Fe Institute, Santa Fe, NM, USA.
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5
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Oh S, Cho K, Park S, Kwon MJ, Chung J, Lee S. Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130413. [PMID: 36436452 DOI: 10.1016/j.jhazmat.2022.130413] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.
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Affiliation(s)
- Sungjik Oh
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Saerom Park
- Urban Water Circulation Research Center, Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jaeshik Chung
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea.
| | - Seunghak Lee
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea; Graduate School of Energy and Environment (KU-KIST Green School), Korea University, Seoul 02841, South Korea.
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6
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Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau. Toxins (Basel) 2021; 13:toxins13120894. [PMID: 34941731 PMCID: PMC8704429 DOI: 10.3390/toxins13120894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/13/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.
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7
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Johnson ACB, Biddle AS. A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure. Animals (Basel) 2021; 11:ani11071975. [PMID: 34359102 PMCID: PMC8300108 DOI: 10.3390/ani11071975] [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: 05/07/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Horses with different metabolic tendencies are anecdotally referred to as “easy” or “hard” keepers. Easy keepers tend to gain weight easily while hard keepers require extra feed to maintain condition. Both easy and hard keeper horses carry a managerial and financial burden which can be a dissuading factor for horse shoppers. This research uses energy intake/need and body condition to develop a standard Equine Keeper Status Scale (EKSS) for assigning keeper status. The microbiome compositions based on EKSS assignments are then compared to explore microbiome differences based on metabolic tendencies of each group. The EKSS can be used by owners to accurately assess their horses’ metabolic tendencies and make improved feeding decisions to meet their horses’ needs. Understanding microbiome differences between easy, medium and hard keeper horses points to potential microbial roles in these metabolic tendencies. Abstract Thriftiness in horses has been associated with more efficient nutrient harvesting in digestion, absorption and/or utilization, but the relative contribution of the gut microbiome to host metabolic tendency is not well understood. Recognizing the unreliability of owner reported assignment of keeper status, this research describes a novel tool for calculating whether a horse is an easy (EK) or hard (HK) keeper and then characterizes microbiome differences in these groups. The Equine Keeper Status Scale (EKSS) was developed and validated based on data gathered from 240 horses. Estimates of dietary energy intakes and requirements to achieve the optimal BCS score of 5 were used in EKSS assignments. Sixty percent of owners’ characterizations disagreed with EKSS identified keeper assignments. Equine fecal 16S rRNA profiles (n = 73) revealed differences in α and β diversities and taxa abundances based on EKSS assignments. EK communities had more Planctomycetes and fewer Euryarcheaota, Spirochaetes and Proteobacteria than HK indicating functional differences in nutrient harvesting between groups. Differences in the gut microbiomes of horses based on keeper assignment point to host/microbial interactions that may underlie some differences in metabolic tendency. The EKSS enables robust, repeatable determination of keeper status which can be used by researchers and horse owners.
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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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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10
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Pin L, Eiler A, Fazi S, Friberg N. Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators. Mol Ecol Resour 2021; 21:1200-1215. [PMID: 33529477 DOI: 10.1111/1755-0998.13341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 01/04/2023]
Abstract
Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD-FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD-FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta-dispersion analyses on both CARD-FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD-FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD-FISH for large scale bio-assessment.
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Affiliation(s)
- Lorenzo Pin
- Norsk Institutt for Vannforskning (NIVA), Oslo, Norway.,Section for Aquatic Biology and Toxicology, Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, Norway
| | - Alexander Eiler
- Section for Aquatic Biology and Toxicology, Department of Biosciences, Centre for Biogeochemistry in the Anthropocene, University of Oslo, Norway.,eDNA solutions AB, Mölndal, Sweden
| | - Stefano Fazi
- Water Research Institute, IRSA-CNR, Monterotondo, Roma, Italy
| | - Nikolai Friberg
- Norsk Institutt for Vannforskning (NIVA), Oslo, Norway.,Freshwater Biological Section, University of Copenhagen, Copenhagen, Denmark.,School of Geography, University of Leeds, Leeds, UK
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11
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Juvigny‐Khenafou NPD, Piggott JJ, Atkinson D, Zhang Y, Macaulay SJ, Wu N, Matthaei CD. Impacts of multiple anthropogenic stressors on stream macroinvertebrate community composition and functional diversity. Ecol Evol 2021; 11:133-152. [PMID: 33437419 PMCID: PMC7790656 DOI: 10.1002/ece3.6979] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 10/13/2020] [Indexed: 01/25/2023] Open
Abstract
Ensuring the provision of essential ecosystem services in systems affected by multiple stressors is a key challenge for theoretical and applied ecology. Trait-based approaches have increasingly been used in multiple-stressor research in freshwaters because they potentially provide a powerful method to explore the mechanisms underlying changes in populations and communities. Individual benthic macroinvertebrate traits associated with mobility, life history, morphology, and feeding habits are often used to determine how environmental drivers structure stream communities. However, to date multiple-stressor research on stream invertebrates has focused more on taxonomic than on functional metrics. We conducted a fully crossed, 4-factor experiment in 64 stream mesocosms fed by a pristine montane stream (21 days of colonization, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation on invertebrate community, taxon, functional diversity and trait variables after 2 and 3 weeks of stressor exposure. 89% of the community structure metrics, 59% of the common taxa, 50% of functional diversity metrics, and 79% of functional traits responded to at least one stressor each. Deposited fine sediment and flow velocity reduction had the strongest impacts, affecting invertebrate abundances and diversity, and their effects translated into a reduction of functional redundancy. Stressor effects often varied between sampling occasions, further complicating the prediction of multiple-stressor effects on communities. Overall, our study suggests that future research combining community, trait, and functional diversity assessments can improve our understanding of multiple-stressor effects and their interactions in running waters.
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Affiliation(s)
- Noel P. D. Juvigny‐Khenafou
- Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolUK
- Department of Health and Environmental SciencesXi'an Jiaotong‐Liverpool UniversityJiangsuChina
- iES – Institute for Environmental Sciences LandauUniversity Koblenz‐LandauLandauGermany
| | - Jeremy J. Piggott
- Trinity Centre for the Environment & Department of ZoologySchool of Natural SciencesTrinity College DublinThe University of DublinDublinIreland
| | - David Atkinson
- Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolUK
| | - Yixin Zhang
- Department of Landscape ArchitectureGold Mantis School of ArchitectureSoochow UniversitySuzhouChina
| | | | - Naicheng Wu
- Department of Health and Environmental SciencesXi'an Jiaotong‐Liverpool UniversityJiangsuChina
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12
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Yao D, Xu L, Wang C. Diversity of the microbial community and antioxidant activity during fermentation of red raspberry Enzymes. Food Sci Nutr 2021; 9:99-110. [PMID: 33473274 PMCID: PMC7802569 DOI: 10.1002/fsn3.1961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 10/08/2020] [Indexed: 12/26/2022] Open
Abstract
The diversity and succession of microbial community and antioxidant activity present during the preparation of red raspberry Enzymes with and without starter cultures were investigated by high-throughput sequencing of 16S rRNA and ITS1 genes and correlation analysis of the microbial diversity and antioxidant activity. The results showed that the sample inoculated with mixed fermentation had higher antioxidant activity than the sample without inoculated fermentation. The antioxidant capacity of red raspberry Enzymes increased significantly as the fermentation time increased. Firmicutes and Ascomycota were the predominant phyla of bacteria and fungi in all samples. At the genus level, Rhodococcus and Lactobacillus were the predominating bacteria throughout the fermentation process. The genus Kodamaea dominated the fungal community of early-fermentation samples with microbial inoculated fermentation. Candida spp. grew rapidly in the late stage of fermentation in the samples with spontaneous fermentation. Unweighted pair-group and PCA analysis revealed that the microbiota structures differed between the two groups. RDA and CCA showed that Rhodococcus and Kodamaea had positive effects on the DPPH scavenging ability and other antioxidant indicators, and the total phenol content had a significant and positive correlation coefficient with Gluconobacter. The results indicated that the fermentation by microorganisms significantly improves the oxidation resistance and helps to improve the quality of the red raspberry Enzymes.
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Affiliation(s)
- Di Yao
- Department of Food Science and EngineeringCollege of FoodHeilongjiang Bayi Agricultural UniversityDaqingChina
| | - Lei Xu
- Department of Food Science and EngineeringCollege of FoodHeilongjiang Bayi Agricultural UniversityDaqingChina
| | - Changyuan Wang
- Department of Food Science and EngineeringCollege of FoodHeilongjiang Bayi Agricultural UniversityDaqingChina
- Department of National Coarse Cereals Engineering Research CenterHeilongjiang Bayi Agricultural UniversityDaqingChina
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13
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Juvigny-Khenafou NPD, Piggott JJ, Atkinson D, Zhang Y, Wu N, Matthaei CD. Fine sediment and flow velocity impact bacterial community and functional profile more than nutrient enrichment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02212. [PMID: 32754996 DOI: 10.1002/eap.2212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Freshwater ecosystems face many simultaneous pressures due to human activities. Consequently, there has been a rapid loss of freshwater biodiversity and an increase in biomonitoring programs. Our study assessed the potential of benthic stream bacterial communities as indicators of multiple-stressor impacts associated with urbanization and agricultural intensification. We conducted a fully crossed four-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 d of colonization, 21 d of manipulations) and investigated the effects of nutrient enrichment, flow-velocity reduction and added fine sediment after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S rRNA genes), as well as curated biological databases (METAGENassit, MetaCyc), to identify changes in bacterial relative abundances and predicted metabolic functional profile. Sediment addition and flow-velocity reduction were the most pervasive stressors. They both increased α-diversity and had strong taxon-specific effects on community composition and predicted functions. Sediment and flow velocity also interacted frequently, with 88% of all bacterial response variables showing two-way interactions and 33% showing three-way interactions including nutrient enrichment. Changes in relative abundances of common taxa were associated with shifts in dominant predicted functions, which can be extrapolated to underlaying stream-wide mechanisms such as carbon use and bacterial energy production pathways. Observed changes were largely stable over time and occurred after just 2 weeks of exposure, demonstrating that bacterial communities can be well-suited for early detection of multiple stressors. Overall, added sediment and reduced flow velocity impacted both bacterial community structure and predicted function more than nutrient enrichment. In future research and stream management, a holistic approach to studying multiple-stressor impacts should include multiple trophic levels with their functional responses, to enhance our mechanistic understanding of complex stressor effects and promote establishment of more efficient biomonitoring programs.
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Affiliation(s)
- Noël P D Juvigny-Khenafou
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road Suzhou, Jiangsu, 215123, China
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Yixin Zhang
- Department of Landscape Architecture, Soochow University, Suzhou, 215123, China
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road Suzhou, Jiangsu, 215123, China
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
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14
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Renes SE, Sjöstedt J, Fetzer I, Langenheder S. Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances. Sci Rep 2020; 10:11333. [PMID: 32647292 PMCID: PMC7347917 DOI: 10.1038/s41598-020-68104-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 02/08/2023] Open
Abstract
Climate change is expected to increase the incidences of extremes in environmental conditions. To investigate how repeated disturbances affect microbial ecosystem resistance, natural lake bacterioplankton communities were subjected to repeated temperature disturbances of two intensities (25 °C and 35 °C), and subsequently to an acidification event. We measured functional parameters (bacterial production, abundance, extracellular enzyme activities) and community composition parameters (richness, evenness, niche width) and found that, compared to undisturbed control communities, the 35 °C treatment was strongly affected in all parameters, while the 25 °C treatment did not significantly differ from the control. Interestingly, exposure to multiple temperature disturbances caused gradually increasing stability in the 35 °C treatment in some parameters, while others parameters showed the opposite, indicating that the choice of parameters can strongly affect the outcome of a study. The acidification event did not lead to stronger changes in community structure, but functional resistance of bacterial production towards acidification in the 35 °C treatments increased. This indicates that functional resistance in response to a novel disturbance can be increased by previous exposure to another disturbance, suggesting similarity in stress tolerance mechanisms for both disturbances. These results highlight the need for understanding function- and disturbance-specific responses, since general responses are likely to be unpredictable.
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Affiliation(s)
- Sophia Elise Renes
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden. .,Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden.
| | - Johanna Sjöstedt
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden. .,Department of Biology/Aquatic Ecology, Lund University, Lund, Sweden.
| | - Ingo Fetzer
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.,Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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15
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Lanzén A, Mendibil I, Borja Á, Alonso-Sáez L. A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay. Mol Ecol 2020; 30:2969-2987. [PMID: 32479653 DOI: 10.1111/mec.15489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost-prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross-validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats.
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Affiliation(s)
- Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Ángel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
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16
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Multiple Stressors Determine Community Structure and Estimated Function of River Biofilm Bacteria. Appl Environ Microbiol 2020; 86:AEM.00291-20. [PMID: 32245764 DOI: 10.1128/aem.00291-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/28/2020] [Indexed: 11/20/2022] Open
Abstract
Freshwater ecosystems are exposed to multiple stressors, but their individual and combined effects remain largely unexplored. Here, we investigated the response of stream biofilm bacterial communities to warming, hydrological stress, and pesticide exposure. We used 24 artificial streams on which epilithic (growing on coarse sediments) and epipsammic (growing on fine sediments) stream biofilms were maintained. Bacterial community composition and estimated function of biofilms exposed during 30 days to individual and combined stressors were assessed using 16S rRNA gene metabarcoding. Among the individual effects by stressors, hydrological stress (i.e., a simulated low-flow situation) was the most relevant, since it significantly altered 57% of the most abundant bacterial taxa (n = 28), followed by warming (21%) and pesticide exposure (11%). Regarding the combined effects, 16% of all stressor combinations resulted in significant interactions on bacterial community composition and estimated function. Antagonistic responses prevailed (57 to 89% of all significant interactions), followed by synergisms (11 to 43%), on specific bacterial taxa, indicating that multiple-stressor scenarios could lead to unexpected shifts in the community composition and associated functions of riverine bacterial communities.IMPORTANCE Freshwater ecosystems such as rivers are of crucial importance for human well-being. However, human activities result in many stressors (e.g., toxic chemicals, increased water temperatures, and hydrological alterations) cooccurring in rivers and streams worldwide. Among the many organisms inhabiting rivers and streams, bacteria are ecologically crucial; they are placed at the base of virtually all food webs and they recycle the organic matter needed for bigger organisms. Most of these bacteria are in close contact with river substratum, where they form the biofilms. There is an urgent need to evaluate the effects of these stressors on river biofilms, so we can anticipate future environmental problems. In this study, we experimentally exposed river biofilms to a pesticide mixture, an increase in water temperature and a simulated low-flow condition, in order to evaluate the individual and joint effects of these stressors on the bacterial community composition and estimated function.
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17
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Zhao Y, Liu H, Wang R, Wu C. Interactions between dicyandiamide and periphytic biofilms in paddy soils and subsequent effects on nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 718:137417. [PMID: 32105918 DOI: 10.1016/j.scitotenv.2020.137417] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Dicyandiamide (DCD) is commonly used as nitrification inhibitors which has the potential to reduce nitrogen loss from paddy soils. In paddy systems, periphytic biofilms are commonly presented at the soil/water interface and show significant effects on nutrient cycling. However, the interaction between DCD and periphytic biofilms in paddy and subsequent effects on nitrogen cycling is unclear. In this work, microcosm experiments were carried out to study the interaction between the periphytic biofilms and DCD and the potential influence on nitrogen cycling from in paddy. Results showed that DCD affected the development of periphytic biofilms, while the presence of periphytic biofilms accelerated DCD degradation. Results also showed DCD application reduced nitrification potential mainly by inhibiting ammonia-oxidizing bacteria (AOB). Higher DCD dosage increased NH3 volatilization loss. However, presence of periphytic biofilm reduced the NH3 volatilization loss but increased denitrification. Our work contributes to a better understanding on the nitrogen cycling processes in paddy, and provides useful information for the improvement of nitrogen utilization efficiency and the control of non-point source pollution.
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Affiliation(s)
- Yanhui Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Environmental Monitoring and Scientific Research of Yangtze River Basin Ecology and Environment Administration, Ministry of Ecology and Environment of the People's Republic of China, Wuhan 430019, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huafeng Liu
- Shandong Institute of Geological Survey, Jinan 250014, China
| | - Renyong Wang
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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18
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Juvigny-Khenafou NPD, Zhang Y, Piggott JJ, Atkinson D, Matthaei CD, Van Bael SA, Wu N. Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:135053. [PMID: 31859062 DOI: 10.1016/j.scitotenv.2019.135053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.
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Affiliation(s)
- Noël P D Juvigny-Khenafou
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK; Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Yixin Zhang
- Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, China.
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St. Charles Avenue, Boggs 400, New Orleans, LA 70118, USA
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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19
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Orr JA, Vinebrooke RD, Jackson MC, Kroeker KJ, Kordas RL, Mantyka-Pringle C, Van den Brink PJ, De Laender F, Stoks R, Holmstrup M, Matthaei CD, Monk WA, Penk MR, Leuzinger S, Schäfer RB, Piggott JJ. Towards a unified study of multiple stressors: divisions and common goals across research disciplines. Proc Biol Sci 2020; 287:20200421. [PMID: 32370677 DOI: 10.1098/rspb.2020.0421] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Anthropogenic environmental changes, or 'stressors', increasingly threaten biodiversity and ecosystem functioning worldwide. Multiple-stressor research is a rapidly expanding field of science that seeks to understand and ultimately predict the interactions between stressors. Reviews and meta-analyses of the primary scientific literature have largely been specific to either freshwater, marine or terrestrial ecology, or ecotoxicology. In this cross-disciplinary study, we review the state of knowledge within and among these disciplines to highlight commonality and division in multiple-stressor research. Our review goes beyond a description of previous research by using quantitative bibliometric analysis to identify the division between disciplines and link previously disconnected research communities. Towards a unified research framework, we discuss the shared goal of increased realism through both ecological and temporal complexity, with the overarching aim of improving predictive power. In a rapidly changing world, advancing our understanding of the cumulative ecological impacts of multiple stressors is critical for biodiversity conservation and ecosystem management. Identifying and overcoming the barriers to interdisciplinary knowledge exchange is necessary in rising to this challenge. Division between ecosystem types and disciplines is largely a human creation. Species and stressors cross these borders and so should the scientists who study them.
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Affiliation(s)
- James A Orr
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Rolf D Vinebrooke
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Kristy J Kroeker
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Rebecca L Kordas
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Berkshire, UK
| | - Chrystal Mantyka-Pringle
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Wildlife Conservation Society Canada, Whitehorse, Yukon Territory, Canada
| | - Paul J Van den Brink
- Aquatic Ecology and Water Quality Management Group, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands.,Wageningen Environmental Research, PO Box 47, 6700 AA Wageningen, The Netherlands
| | - Frederik De Laender
- Research Unit of Environmental and Evolutionary Biology, Namur Institute of Complex Systems, and Institute of Life, Earth, and the Environment, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Robby Stoks
- Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | | | | | - Wendy A Monk
- Environment and Climate Change Canada at Canadian Rivers Institute, Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Marcin R Penk
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Sebastian Leuzinger
- Institute for Applied Ecology, Auckland University of Technology, Auckland, New Zealand
| | - Ralf B Schäfer
- Quantitative Landscape Ecology, iES-Institute for Environmental Sciences, University Koblenz-Landau, Landau in der Pfalz, Germany
| | - Jeremy J Piggott
- School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
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20
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Meng L, Zuo R, Wang JS, Yang J, Li Q, Chen M. The spatial variations of correlation between microbial diversity and groundwater quality derived from a riverbank filtration site, northeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135855. [PMID: 31864995 DOI: 10.1016/j.scitotenv.2019.135855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/03/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
To identify the relationship between microbial communities and groundwater quality parameters, especially typical groundwater contaminants including ammonium (NH4+), iron (Fe2+), and manganese (Mn2+), groundwater samples and aquifer media were collected from a riverbank filtration (RBF) site in Harbin city, northeast China. The structures of the microbial communities of aquifer media at different depths were illustrated through 16S rRNA sequencing using the Illumina MiSeq platform, and the correlation between microbial communities and water quality parameters was quantitatively demonstrated by redundancy analysis (RDA). The results revealed that the diversity of microbial communities decreased along the groundwater flow path at the south bank of Songhua river. The richness and diversity in the unsaturated zone (0-5 m) were significantly higher than those in the saturated zone (5-50 m) because of physiochemical properties of aquifer media and the redox environment in the RBF system. Core taxa, which were significantly related to the biotransformation behavior of iron, manganese, and ammonium, were Pseudomonas, Acinetobacter, Ochrobactrum, Sphingobium, and Sphingomonas. RDA results indicated that the critical physiochemical parameters that significantly influenced the composition of microbial communities were different in the saturated and unsaturated zones, and the total organic carbon (TOC), electrical conductivity (EC), nitrate (NO3-), and manganese (Mn2+) levels were the four principal factors affecting the function and composition of microbial communities in the whole RBF system. Proteobacteria, Sphingomonadales, and Sphingobium were the dominant bacteria at the phylum, order, and genus levels with 39.8%, 59.2%, and 65.3% contribution to the overall groundwater quality, respectively. The results obtained from this study should improve the understanding of the relationship between the structure of microbial communities (especially, bacteria related to the biotransformation of NH4+, Fe2+, and Mn2+) and physiochemical parameters.
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Affiliation(s)
- Li Meng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Rui Zuo
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China.
| | - Jin-Sheng Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Jie Yang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Qiao Li
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
| | - Minhua Chen
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, Beijing 100875, China
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Salis RK, Bruder A, Piggott JJ, Summerfield TC, Matthaei CD. Multiple-stressor effects of dicyandiamide (DCD) and agricultural stressors on trait-based responses of stream benthic algal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 693:133305. [PMID: 31635001 DOI: 10.1016/j.scitotenv.2019.07.111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/05/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Agricultural practices often result in multiple stressors affecting stream ecosystems, and interacting stressors complicate environmental assessment and management of impacted streams. The nitrification inhibitor dicyandiamide (DCD) is used for nitrogen management on farmland. Effects of leached DCD on stream ecosystems are still largely unstudied, even though it could be relevant as a stressor on its own or in combination with other agricultural stressors. We conducted two experiments in 128 outdoor stream-fed mesocosms to assess stressor effects on biomass, cell density, taxon richness, evenness and functional trait composition of benthic algal communities. First, we examined responses to a wide DCD gradient (eight concentrations, 0-31 mg L-1) and two additional stressors, deposited fine sediment (none, high) and nutrient enrichment (ambient, enriched). Second, we determined algal responses to four stressors: DCD, sediment, nutrients, and reduced flow velocity. Here DCD treatments included controls, constant application (1.4 mg L-1) and two pulsed treatments mimicking concentration patterns in real streams (peaks 3.5 mg L-1, 2.2 mg L-1). Sediment and nutrient enrichment were influential stressors in both experiments, with fine sediment having the most pervasive effects. In Experiment 2, reduced flow velocity had pervasive effects and stressor interactions were mainly restricted to two-way interactions. DCD had few, weak stressor main effects, especially at field-realistic concentrations (Experiment 2). At the highest concentrations in Experiment 1 (above levels observed in real streams), DCD effects were still rare but some significant stressor interactions occurred. Analyses of functional traits were helpful in identifying potential mechanisms driving changes in densities and community composition. These findings suggest that, while DCD on its own may be a minor stressor, it could have adverse effects on algal communities already exposed to other stressors, a scenario common in agricultural streams.
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Affiliation(s)
- Romana K Salis
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany.
| | - Andreas Bruder
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Laboratory of Applied Microbiology, University of Applied Sciences and Arts of Southern Switzerland, Via Mirasole 22A, 6500 Bellinzona, Switzerland
| | - Jeremy J Piggott
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - Tina C Summerfield
- Department of Botany, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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22
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Romero F, Acuña V, Font C, Freixa A, Sabater S. Effects of multiple stressors on river biofilms depend on the time scale. Sci Rep 2019; 9:15810. [PMID: 31676856 PMCID: PMC6825187 DOI: 10.1038/s41598-019-52320-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/15/2019] [Indexed: 11/08/2022] Open
Abstract
Global change exposes ecosystems to a myriad of stressors differing in their spatial (i.e. surface of stressed area) and temporal (i.e. exposure time) components. Among freshwater ecosystems, rivers and streams are subject to physical, chemical and biological stressors, which interact with each other and might produce diverging effects depending on exposure time. We conducted a manipulative experiment using 24 artificial streams to examine the individual and combined effects of warming (1.6 °C increase in water temperature), hydrological stress (simulated low-flow situation) and chemical stress caused by pesticide exposure (15.1-156.7 ng L-1) on river biofilms. We examined whether co-occurring stressors could lead to non-additive effects, and if these differed at two different exposure times. Specifically, structural and functional biofilm responses were assessed after 48 hours (short-term effects) and after 30 days (long-term effects) of exposure. Hydrological stress caused strong negative impacts on river biofilms, whereas effects of warming and pesticide exposure were less intense, although increasing on the long term. Most stressor combinations (71%) resulted in non-significant interactions, suggesting overall additive effects, but some non-additive interactions also occurred. Among non-additive interactions, 59% were classified as antagonisms after short-term exposure to the different stressor combinations, rising to 86% at long term. Our results indicate that a 30-day exposure period to multiple stressors increases the frequency of antagonistic interactions compared to a 48-hour exposure to the same conditions. Overall, the impacts of multiple-stressor occurrences appear to be hardly predictable from individual effects, highlighting the need to consider temporal components such as duration when predicting the effects of multiple stressors.
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Affiliation(s)
- Ferran Romero
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003, Girona, Spain.
- Universitat de Girona (UdG), Girona, Spain.
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003, Girona, Spain
- Universitat de Girona (UdG), Girona, Spain
| | - Carme Font
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003, Girona, Spain
- Universitat de Girona (UdG), Girona, Spain
| | - Anna Freixa
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003, Girona, Spain
- Universitat de Girona (UdG), Girona, Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA), C. Emili Grahit 101, 17003, Girona, Spain
- Institute of Aquatic Ecology (IEA), University of Girona, Campus de Montilivi, 17003, Girona, Spain
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23
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Romero F, Sabater S, Font C, Balcázar JL, Acuña V. Desiccation events change the microbial response to gradients of wastewater effluent pollution. WATER RESEARCH 2019; 151:371-380. [PMID: 30616049 DOI: 10.1016/j.watres.2018.12.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
While wastewater treatment plant (WWTP) effluents have become increasingly recognized as a stressor for receiving rivers, their effects on river microbial communities remain elusive. Moreover, global change is increasing the frequency and duration of desiccation events in river networks, and we ignore how desiccation might influence the response of microbial communities to WWTP effluents. In this study, we evaluated the interaction between desiccation events and WWTP effluents under different dilution capacities. Specifically, we used artificial streams in a replicated regressional design, exposing first a section of the streams to a 7-day desiccation period and then the full stream to different levels of a realistic WWTP effluent dilution, from 0% to 100% of WWTP effluent proportion of the total stream flow. The microbial community response was assessed by means of high-throughput sequencing of 16S rRNA gene amplicons and quantitative PCR targeting ecologically-relevant microbial groups. Threshold Indicator Taxa Analysis (TITAN) was used, together with model fitting, to determine community thresholds and potential indicator taxa. Results show significant interactions between WWTP effluents and desiccation, particularly when sediment type is considered. Indicator taxa included members of Proteobacteria, Actinobacteria and Cyanobacteria, with abrupt changes in community structure at WWTP effluent proportion of the total flow above 50%, which is related to nutrient levels ranging 4.6-5.2 mg N-NO3-L-1, 0.21-0.32 mg P-PO43-L-1 and 7.09-9.00 mg DOC L-1. Our work indicates that situations where WWTP effluents account for >50% of the total river flow might risk of dramatic microbial community structure changes and should be avoided.
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Affiliation(s)
- Ferran Romero
- ICRA, Catalan Institute for Water Research, Emili Grahit 101, University of Girona, 17003 Girona Spain.
| | - Sergi Sabater
- ICRA, Catalan Institute for Water Research, Emili Grahit 101, University of Girona, 17003 Girona Spain; Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, Girona 17071 Spain
| | - Carme Font
- ICRA, Catalan Institute for Water Research, Emili Grahit 101, University of Girona, 17003 Girona Spain
| | - José Luís Balcázar
- ICRA, Catalan Institute for Water Research, Emili Grahit 101, University of Girona, 17003 Girona Spain
| | - Vicenç Acuña
- ICRA, Catalan Institute for Water Research, Emili Grahit 101, University of Girona, 17003 Girona Spain
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24
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Lehosmaa K, Jyväsjärvi J, Ilmonen J, Rossi PM, Paasivirta L, Muotka T. Groundwater contamination and land drainage induce divergent responses in boreal spring ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:100-109. [PMID: 29778675 DOI: 10.1016/j.scitotenv.2018.05.126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/30/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
Degradation of freshwater ecosystems has engendered legislative mandates for the protection and management of surface waters while groundwater-dependent ecosystems (GDEs) have received much less attention. This is so despite biodiversity and functioning of GDEs are currently threatened by several anthropogenic stressors, particularly intensified land use and groundwater contamination. We assessed the impacts of land drainage (increased input of dissolved organic carbon, DOC, from peatland drainage) and impaired groundwater chemical quality (NO3--N enrichment from agricultural or urban land use) on biodiversity and ecosystem functioning in 20 southern Finnish cold-water springs using several taxonomic and functional measures. Groundwater contamination decreased macroinvertebrate and bacterial diversity and altered their community composition. Changes in macroinvertebrate and bacterial communities along the gradient of water-quality impairment were caused by the replacement of native with new taxa rather than by mere disappearance of some of the original taxa. Also species richness of habitat specialist (but not headwater generalist) bryophytes decreased due to impaired groundwater quality. Periphyton accrual rate showed a subsidy-stress response to elevated nitrate concentrations, with peak values at around 2500 μg L-1, while drainage-induced spring water brownification (increased DOC) reduced both periphyton accrual and leaf decomposition rates already at very low concentrations. Our results highlight the underutilized potential of ecosystem-level functional measures in GDE bioassessment as they seem to respond to the first signs of spring ecosystem impairment, at least for the anthropogenic stressors studied by us.
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Affiliation(s)
- Kaisa Lehosmaa
- University of Oulu, Department of Ecology and Genetics, P.O. Box 3000, FI-90014 Oulu, Finland.
| | - Jussi Jyväsjärvi
- University of Oulu, Department of Ecology and Genetics, P.O. Box 3000, FI-90014 Oulu, Finland
| | - Jari Ilmonen
- Metsähallitus, P.O. Box 94, FI-01301 Vantaa, Finland
| | - Pekka M Rossi
- Water Resources and Environmental Engineering Research Group, University of Oulu, P.O. Box 3000, FI-90014, Finland
| | | | - Timo Muotka
- University of Oulu, Department of Ecology and Genetics, P.O. Box 3000, FI-90014 Oulu, Finland; Finnish Environment Institute, Natural Environment Centre, FI-90014 Oulu, Finland
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25
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Pawlowski J, Kelly-Quinn M, Altermatt F, Apothéloz-Perret-Gentil L, Beja P, Boggero A, Borja A, Bouchez A, Cordier T, Domaizon I, Feio MJ, Filipe AF, Fornaroli R, Graf W, Herder J, van der Hoorn B, Iwan Jones J, Sagova-Mareckova M, Moritz C, Barquín J, Piggott JJ, Pinna M, Rimet F, Rinkevich B, Sousa-Santos C, Specchia V, Trobajo R, Vasselon V, Vitecek S, Zimmerman J, Weigand A, Leese F, Kahlert M. The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1295-1310. [PMID: 29801222 DOI: 10.1016/j.scitotenv.2018.05.002] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 05/01/2018] [Indexed: 05/05/2023]
Abstract
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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Affiliation(s)
- Jan Pawlowski
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland.
| | - Mary Kelly-Quinn
- School of Biology & Environmental Science, University College Dublin, Ireland
| | - Florian Altermatt
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland(;) Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | - Pedro Beja
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Angela Boggero
- LifeWatch, Italy and CNR-Institute of Ecosystem Study (CNR-ISE), Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Angel Borja
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110 Pasaia, Spain
| | - Agnès Bouchez
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Tristan Cordier
- Department of Genetics and Evolution, University of Geneva, CH-1211 Geneva, Switzerland
| | - Isabelle Domaizon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Maria Joao Feio
- Marine and Environmental Sciences Centre, Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Portugal
| | - Ana Filipa Filipe
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal; CEABN/InBIO-Centro de Estudos Ambientais 'Prof. Baeta Neves', Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Riccardo Fornaroli
- University of Milano Bicocca, Department of Earth and Environmental Sciences(DISAT), Piazza della Scienza 1,20126 Milano, Italy
| | - Wolfram Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), 1180 Vienna, Austria
| | - Jelger Herder
- RAVON, Postbus 1413, Nijmegen 6501 BK, The Netherlands
| | | | - J Iwan Jones
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Marketa Sagova-Mareckova
- Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovska 507, 16106 Praha 6, Czechia
| | - Christian Moritz
- ARGE Limnologie GesmbH, Hunoldstraße 14, 6020 Innsbruck, Austria
| | - Jose Barquín
- Environmental Hydraulics Institute "IHCantabria", Universidad de Cantabria, C/ Isabel Torres n°15, Parque Científico y Tecnológico de Cantabria, 39011 Santander, Spain
| | - Jeremy J Piggott
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, the University of Dublin, College Green, Dublin 2, Ireland; Department of Zoology, University of Otago, 340 Great King Street, Dunedin 9016, New Zealand
| | - Maurizio Pinna
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Frederic Rimet
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Buki Rinkevich
- Israel Oceanographic and Limnological Research, Tel- Shikmona, Haifa 31080, Israel
| | - Carla Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Valeria Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, S.P. Lecce-Monteroni, 73100 Lecce, Italy
| | - Rosa Trobajo
- IRTA, Institute of Agriculture and Food Research and Technology, Marine and Continental Waters Program, Carretera Poble Nou Km 5.5, E-43540 St. Carles de la Ràpita, Catalonia, Spain
| | - Valentin Vasselon
- INRA, UMR42 CARRTEL, 75bis Avenue de Corzent, 74203 Thonon les Bains Cedex, France
| | - Simon Vitecek
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jonas Zimmerman
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany
| | - Alexander Weigand
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany; Musée National d'Histoire Naturelle, 25 Rue Münster, 2160 Luxembourg, Luxembourg
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE - 750 07 Uppsala, Sweden
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26
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Nuy JK, Lange A, Beermann AJ, Jensen M, Elbrecht V, Röhl O, Peršoh D, Begerow D, Leese F, Boenigk J. Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:1287-1301. [PMID: 29758882 DOI: 10.1016/j.scitotenv.2018.03.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances.
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Affiliation(s)
- Julia K Nuy
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Anja Lange
- Department of Bioinformatics and Computational Biophysics, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Arne J Beermann
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Manfred Jensen
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Oliver Röhl
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Derek Peršoh
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
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27
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Sjöstedt J, Langenheder S, Kritzberg E, Karlsson CMG, Lindström ES. Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:493-500. [PMID: 29733107 DOI: 10.1111/1758-2229.12656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/11/2016] [Indexed: 05/25/2023]
Abstract
Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.
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Affiliation(s)
- Johanna Sjöstedt
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
- Department of Biology/Aquatic Ecology, Lund University, Lund, Sölvegatan 37, SE 22362, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
| | - Emma Kritzberg
- Department of Biology/Aquatic Ecology, Lund University, Lund, Sölvegatan 37, SE 22362, Sweden
| | - Christofer M G Karlsson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE 39231, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
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28
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Liu J, Li C, Jing J, Zhao P, Luo Z, Cao M, Ma Z, Jia T, Chai B. Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage. WATER RESEARCH 2018; 133:99-109. [PMID: 29367051 DOI: 10.1016/j.watres.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Environmental gradient have strong effects on community assembly processes. In order to reveal the effects of alkaline mine drainage (AlkMD) on bacterial and denitrifying bacterial community compositions and diversity in tailings reservoir, here we conducted an experiment to examine all and core bacterial taxa and denitrifying functional genes's (nirS, nirK, nosZΙ) abundance along a chemical gradient in tailings water in Shibahe copper tailings in Zhongtiaoshan, China. Differences in bacterial and denitrifying bacterial community compositions in different habitats and their relationships with environmental parameters were analyzed. The results showed that the richness and diversity of bacterial community in downstream seeping water (SDSW) were the largest, while that in upstream tailings water (STW1) were the lowest. The diversity and abundance of bacterial communities tended to increase from STW1 to SDSW. The variation of bacterial community diversity was significantly related to electroconductibility (EC), nitrate (NO3-), nitrite (NO2-), total carbon (TC), inorganic carbon (IC) and sulfate (SO42-), but was not correlated with geographic distance in local scale. Core taxa from class to genus were all significantly related to NO3- and NO2-. Core taxa Rhodobacteraceae, Rhodobacter, Acinetobacter and Hydrogenophaga were typical denitrifying bacteria. The variation trends of these groups were consistent with the copy number of nirS, nirK and nosZΙ, demonstrating their importance in the process of nitrogen reduction. The copy number of nirK, nosZΙ and nirS/16S rDNA, nirK/16Sr DNA correlated strongly with NO3-, NO2- and IC, but nirS and nosZI/16SrDNA had no significant correlation with NO3- and NO2-. The copy numbers of denitrifying functional genes (nirS, nirK and nosZΙ) were negatively correlated with heavy metal plumbum (Pb) and zinc (Zn). It showed that heavy metal contamination was an important factor affecting the structure of denitrifying bacterial community in AlkMD. In this study we have identified the distribution pattern of bacterial community along physiochemical gradients in alkaline tailings reservoir and displayed the driving force of shaping the structure of bacterial community. The influence of NO3-, NO2-, IC and heavy metal Pb and Zn on bacterial community might via their influence on the functional groups involving nitrogen, carbon and metal metabolisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, 030006, China
| | - Juhui Jing
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Miaowen Cao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhuanzhuan Ma
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China.
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