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Tian J, Huang X, Chen H, Kang X, Wang Y. Homogeneous selection is stronger for fungi in deeper peat than in shallow peat in the low-temperature fens of China. ENVIRONMENTAL RESEARCH 2022; 212:113312. [PMID: 35513061 DOI: 10.1016/j.envres.2022.113312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Peatlands have accumulated enormous amounts of carbon over millennia, and climate changes threatens the release of this carbon into the atmosphere. Fungi are crucial drivers of global carbon cycling because they are the principal decomposer of organic matter in peatlands. However, the fungal community composition and ecological preferences in peat remain unclear, which restricts our ability to evaluate the role of the fungal community in peat biogeochemical functions. We investigated 54 soils from 6 low-temperature peatlands across China to fill this knowledge gap. The peat was divided into above-water table (AWT) and below-water table (BWT) layers based on the water table fluctuation. We investigated fungal community assembly processes and drivers for each peat layer. The results showed that fungal communities differed significantly among peat layers. The relative abundance of symbiotrophs was significantly higher in the AWT (17.4%) than in the BWT (9.0%), while the abundances of yeast and litter saprotrophs were obviously lower in the AWT than in the BWT. Our results revealed that the assemblage of both fungal taxonomic and phylogenetic communities was mainly governed by stochastic processes in both AWT (87.8%) and BWT (58.6%) layers. However, in the BWT, the relative importance of deterministic processes (28.4%) significantly increased, indicating a potential deterministic environmental selection induced by permanently anaerobic condition. Mean annual precipitation and mean annual temperature were the most critical drives for the assemblage of the fungal community in the BWT. These observations collectively indicate that fungal community assembly is depth-dependent, implying different community assembly mechanisms and ecological functions along the peat profile. These findings highlight the importance of climate driven deep peat fungal community composition assemblages and suggest the potential to project the changes in fungal diversity with ongoing climate change.
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Affiliation(s)
- Jianqing Tian
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xinya Huang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Xiaoming Kang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yanfen Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Vila-Costa M, Lundin D, Casamayor EO, Meijer SN, Fernández P, Dachs J. Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 308:119592. [PMID: 35688389 DOI: 10.1016/j.envpol.2022.119592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/20/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.
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Affiliation(s)
- Maria Vila-Costa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain.
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Sweden
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes, CEAB-CSIC, Blanes, Catalunya, Spain
| | - Sandra N Meijer
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pilar Fernández
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Jordi Dachs
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
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3
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Biological Microbial Interactions from Cooccurrence Networks in a High Mountain Lacustrine District. mSphere 2022; 7:e0091821. [PMID: 35642514 PMCID: PMC9241510 DOI: 10.1128/msphere.00918-21] [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] [Indexed: 11/20/2022] Open
Abstract
A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed coexisting. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, where biotic interactions might be required to make the most of an extreme environment. We studied a high-throughput gene data set of alpine lakes (>220 Pyrenean lakes) with cooccurrence network analysis to infer potential biotic interactions, using the combination of a probabilistic method for determining significant cooccurrences and coexclusions between pairs of species and a conceptual framework for classifying the nature of the observed cooccurrences and coexclusions. This computational approach (i) determined and quantified the importance of environmental variables and spatial distribution and (ii) defined potential interacting microbial assemblages. We determined the properties and relationships between these assemblages by examining node properties at the taxonomic level, indicating associations with their potential habitat sources (i.e., aquatic versus terrestrial) and their functional strategies (i.e., parasitic versus mixotrophic). Environmental variables explained fewer pairs in bacteria than in microbial eukaryotes for the alpine data set, with pH alone explaining the highest proportion of bacterial pairs. Nutrient composition was also relevant for explaining association pairs, particularly in microeukaryotes. We identified a reduced subset of pairs with the highest probability of species interactions (“interacting guilds”) that significantly reached higher occupancies and lower mean relative abundances in agreement with the carrying capacity hypothesis. The interacting bacterial guilds could be more related to habitat and microdispersal processes (i.e., aquatic versus soil microbes), whereas for microeukaryotes trophic roles (osmotrophs, mixotrophs, and parasitics) could potentially play a major role. Overall, our approach may add helpful information to guide further efforts for a mechanistic understanding of microbial interactions in situ. IMPORTANCE A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed to coexist. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, in which biotic interactions might be required to make the most of an extreme environment. Microbial metacommunities are too often only studied in terms of their environmental niches and geographic barriers since they show inherent difficulties to quantify biological interactions and their role as drivers of ecosystem functioning. Our study highlights that telling apart potential interactions from both environmental and geographic niches may help for the initial characterization of organisms with similar ecologies in a large scope of ecosystems, even when information about actual interactions is partial and limited. The multilayered statistical approach carried out here offers the possibility of going beyond taxonomy to understand microbiological behavior in situ.
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Marasco R, Fusi M, Rolli E, Ettoumi B, Tambone F, Borin S, Ouzari HI, Boudabous A, Sorlini C, Cherif A, Adani F, Daffonchio D. Aridity modulates belowground bacterial community dynamics in olive tree. Environ Microbiol 2021; 23:6275-6291. [PMID: 34490977 PMCID: PMC9290347 DOI: 10.1111/1462-2920.15764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant‐associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co‐occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity‐winner and aridity‐loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co‐occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity‐winners or aridity‐losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Besma Ettoumi
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Fulvia Tambone
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla Lab, University of Milano, Milan, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Hadda-Imene Ouzari
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Abdellatif Boudabous
- Laboratoire Microorganismes et Biomolécules Actives (LR03ES03), Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Claudia Sorlini
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Milan, Italy
| | - Ameur Cherif
- Institut Supérieur de Biotechnologie Sidi Thabet (ISBST), BVBGR-LR11ES31, Biotechpole Sidi Thabet, University Manouba, Ariana, Tunisia
| | - Fabrizio Adani
- Department of Agricultural and Environmental Sciences (DiSAA), Gruppo Ricicla Lab, University of Milano, Milan, Italy
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Dickey JR, Swenie RA, Turner SC, Winfrey CC, Yaffar D, Padukone A, Beals KK, Sheldon KS, Kivlin SN. The Utility of Macroecological Rules for Microbial Biogeography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.
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Ortiz‐Álvarez R, Cáliz J, Camarero L, Casamayor EO. Regional community assembly drivers and microbial environmental sources shaping bacterioplankton in an alpine lacustrine district (Pyrenees, Spain). Environ Microbiol 2019; 22:297-309. [DOI: 10.1111/1462-2920.14848] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Rüdiger Ortiz‐Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Joan Cáliz
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
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7
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Menéndez-Serra M, Triadó-Margarit X, Castañeda C, Herrero J, Casamayor EO. Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:343-353. [PMID: 30199680 DOI: 10.1016/j.scitotenv.2018.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Soil microbial communities (both Bacteria and Archaea) were studied after 16S rRNA genes massive sequencing in two hypersaline and gypsum-rich contrasted sites located in NE Spain. Soil microbial communities were also locally analysed according to environmental variables, including geological, physico-chemical, biogeochemically, and climatic data. Typical soil characteristics, climate data, and plant composition clearly split the two sites and major differences among the microbial communities for the areas were initially expected. Overall, high values of microbial species richness (up to 2300 taxa) and ecological diversity was detected in both sites. High genetic novelty levels were found mostly to environmental sequences, highlighting the high potential for microbiological studies. In contrast to the initial expectations, a substantial overlapping between Monegros and Gallocanta microbes was observed, indicating a high similarity despite of the geographical, botanical and environmental distances between sites, in agreement with both high dispersal and local selection inherent to the microbial world. The potential biogeochemical cycling showed small differences between sites, with presence of photosynthetic green and purple sulfur bacteria, cyanobacteria and aerobic and anaerobic chemolitotrophs. Potential for aerobic methane oxidation and anaerobic methanogenesis was observed in both sites, with predominance of potential nitrification mostly by ammonia-oxidizing archaea, nitrite oxidation and denitrification, and minor contribution for nitrate reduction and nitrate ammonification. The predicted functions based on the taxonomic composition showed high overlapping between the two studied regions, despite their difference in gypsum richness.
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Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Carmen Castañeda
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Juan Herrero
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain.
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8
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Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR, Weaver L. Towards robust and repeatable sampling methods in eDNA-based studies. Mol Ecol Resour 2018; 18:940-952. [PMID: 29802793 DOI: 10.1111/1755-0998.12907] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/28/2023]
Abstract
DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods and inappropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.
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Affiliation(s)
- Ian A Dickie
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Stephane Boyer
- Institut de Recherche sur la Biologie de l'Insecte - UMR 7261 CNRS, Université de Tours, Tours, France
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - Hannah L Buckley
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Paul P Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, CHARS Campus, Cambridge Bay, NU, Canada
| | | | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Andreas Makiola
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Christchurch, New Zealand
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9
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Pitt A, Schmidt J, Lang E, Whitman WB, Woyke T, Hahn MW. Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 2018; 68:1975-1985. [PMID: 29688164 DOI: 10.1099/ijsem.0.002777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain AP-Melu-1000-B4 was isolated from a lake located in the mountains of the Mediterranean island of Corsica (France). Phenotypic, chemotaxonomic and genomic traits were investigated. Phylogenetic analyses based on 16S rRNA gene sequencing referred the strain to the cryptic species complex PnecC within the genus Polynucleobacter. The strain encoded genes for biosynthesis of proteorhodopsin and retinal. When pelleted by centrifugation the strain showed an intense rose colouring. Major fatty acids were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and summed feature 2 (C16 : 1 isoI and C14 : 0-3OH). The sequence of the 16S rRNA gene contained an indel which was not present in any previously described Polynucleobacter species. Genome sequencing revealed a genome size of 1.89 Mbp and a G+C content of 46.6 mol%. In order to resolve the phylogenetic position of the new strain within subcluster PnecC, its phylogeny was reconstructed from sequences of 319 shared genes. To represent all currently described Polynucleobacter species by whole genome sequences, three type strains were additionally sequenced. Our phylogenetic analysis revealed that strain AP-Melu-100-B4 occupied a basal position compared with previously described PnecC strains. Pairwise determined whole genome average nucleotide identity (gANI) values suggested that strain AP-Melu-1000-B4 represents a new species, for which we propose the name Polynucleobacter meluiroseus sp. nov. with the type strain AP-Melu-1000-B4T (=DSM 103591T=CIP 111329T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - William B Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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10
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Ortiz-Álvarez R, Triadó-Margarit X, Camarero L, Casamayor EO, Catalan J. High planktonic diversity in mountain lakes contains similar contributions of autotrophic, heterotrophic and parasitic eukaryotic life forms. Sci Rep 2018. [PMID: 29535368 PMCID: PMC5849755 DOI: 10.1038/s41598-018-22835-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A rich eukaryotic planktonic community exists in high-mountain lakes despite the diluted, oligotrophic and cold, harsh prevailing conditions. Attempts of an overarching appraisal have been traditionally hampered by observational limitations of small, colorless, and soft eukaryotes. We aimed to uncover the regional eukaryotic biodiversity of a mountain lakes district to obtain general conclusions on diversity patterns, dominance, geographic diversification, and food-web players common to oligotrophic worldwide distributed freshwater systems. An unprecedented survey of 227 high-altitude lakes comprising large environmental gradients was carried out using Illumina massive tag sequencing of the 18S rRNA gene. We observed a large Chrysophyceae dominance in richness, abundance and novelty, and unveiled an unexpected richness in heterotrophic phagotrophs and parasites. In particular, Cercozoa and Chytridiomycota showed diversity features similar to the dominant autotrophic groups. The prominent beta-dispersion shown by parasites suggests highly specific interactions and a relevant role in food webs. Interestingly, the freshwater Pyrenean metacommunity contained more diverse specific populations than its closest marine oligotrophic equivalent, with consistently higher beta-diversity. The relevance of unseen groups opens new perspectives for the better understanding of planktonic food webs. Mountain lakes, with remarkable environmental idiosyncrasies, may be suitable environments for the genetic diversification of microscopic eukaryotic life forms.
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Affiliation(s)
- Rüdiger Ortiz-Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain.
| | - Jordi Catalan
- CREAF - CSIC, Campus UAB, Edifici C, 08193, Cerdanyola del Vallès, Catalonia, Spain
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11
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Huggett MJ, Kavazos CRJ, Bernasconi R, Czarnik R, Horwitz P. Bacterioplankton assemblages in coastal ponds reflect the influence of hydrology and geomorphological setting. FEMS Microbiol Ecol 2017; 93:3828103. [PMID: 28505366 DOI: 10.1093/femsec/fix067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/14/2017] [Indexed: 02/01/2023] Open
Abstract
The factors that shape microbial community assembly in aquatic ecosystems have been widely studied; yet it is still unclear how distinct communities within a connected landscape influence one another. Coastal lakes are recipients of, and thus are connected to, both marine and terrestrial environments. Thus, they may host microbial assemblages that reflect the relative degree of influence by, and connectivity to, either system. In order to address this idea, we interrogated microbial community diversity at 49 sites in seven ponds in two seasons in the Lake MacLeod basin, a system fed by seawater flowing inland through underground karst. Environmental and spatial variation within ponds explain <9% of the community structure, while identity of the pond that samples were taken from explains 50% of community variation. That is, ponds each host distinct assemblages despite similarities in size, environment and position in the landscape, indicating a dominant role for local species sorting. The ponds contain a substantial amount of previously unknown microbial taxa, reflecting the unusual nature of this inland system. Rare marine taxa, possibly dispersed from seawater assemblages via the underground karst connection, are abundant within the inland system, suggesting an important role for regional dispersal within the metacommunities.
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Affiliation(s)
- Megan J Huggett
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Christopher R J Kavazos
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Robert Czarnik
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Pierre Horwitz
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
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Some Mixotrophic Flagellate Species Selectively Graze on Archaea. Appl Environ Microbiol 2016; 83:AEM.02317-16. [PMID: 27815273 DOI: 10.1128/aem.02317-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups. IMPORTANCE That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems.
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Ortiz-Alvarez R, Casamayor EO. High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:210-7. [PMID: 26711582 DOI: 10.1111/1758-2229.12370] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 12/16/2015] [Indexed: 05/12/2023]
Abstract
We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.
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Affiliation(s)
- Rudiger Ortiz-Alvarez
- Integrative Freshwater Ecology Group-Limnological Observatory of the Pyrenees, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Blanes, Catalonia, 17300, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group-Limnological Observatory of the Pyrenees, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Blanes, Catalonia, 17300, Spain
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Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. MICROBIAL ECOLOGY 2016; 71:566-574. [PMID: 26552395 DOI: 10.1007/s00248-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.
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Affiliation(s)
- Tomàs Llorens-Marès
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Carles M Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain.
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Daniel ADC, Pedrós-Alió C, Pearce DA, Alcamí A. Composition and Interactions among Bacterial, Microeukaryotic, and T4-like Viral Assemblages in Lakes from Both Polar Zones. Front Microbiol 2016; 7:337. [PMID: 27047459 PMCID: PMC4796948 DOI: 10.3389/fmicb.2016.00337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/03/2016] [Indexed: 02/01/2023] Open
Abstract
In this study we assess global biogeography and correlation patterns among three components of microbial life: bacteria, microeukaryotes, and T4-like myoviruses. In addition to environmental and biogeographical considerations, we have focused our study on samples from high-latitude pristine lakes from both poles, since these simple island-like ecosystems represent ideal ecological models to probe the relationships among microbial components and with the environment. Bacterial assemblages were dominated by members of the same groups found to dominate freshwater ecosystems elsewhere, and microeukaryotic assemblages were dominated by photosynthetic microalgae. Despite inter-lake variations in community composition, the overall percentages of OTUs shared among sites was remarkable, indicating that many microeukaryotic, bacterial, and viral OTUs are globally-distributed. We observed an intriguing negative correlation between bacterial and microeukaryotic diversity values. Notably, our analyses show significant global correlations between bacterial and microeukaryotic community structures, and between the phylogenetic compositions of bacterial and T4-like virus assemblages. Overall, environmental filtering emerged as the main factor driving community structures.
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Affiliation(s)
- Aguirre de Cárcer Daniel
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain
| | | | - David A Pearce
- British Antarctic Survey, Natural Environment Research CouncilCambridge, UK; Faculty of Health and Life Sciences, University of NorthumbriaNewcastle Upon Tyne, UK; University Center in SvalbardLonyearbyen, Norway
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid Madrid, Spain
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Ruiz-González C, Niño-García JP, del Giorgio PA. Terrestrial origin of bacterial communities in complex boreal freshwater networks. Ecol Lett 2015; 18:1198-1206. [DOI: 10.1111/ele.12499] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/02/2015] [Accepted: 07/24/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Clara Ruiz-González
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL); Département des Sciences Biologiques; Université du Québec à Montréal; Case Postale 8888 Succursale Centre-Ville Montréal QC H3C 3P8 Canada
| | - Juan Pablo Niño-García
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL); Département des Sciences Biologiques; Université du Québec à Montréal; Case Postale 8888 Succursale Centre-Ville Montréal QC H3C 3P8 Canada
- Escuela de Microbiología Universidad de Antioquia Ciudad Universitaria Calle 67 N° 53-108; Medellín Colombia
| | - Paul A. del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL); Département des Sciences Biologiques; Université du Québec à Montréal; Case Postale 8888 Succursale Centre-Ville Montréal QC H3C 3P8 Canada
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