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Gazulla CR, Cabello AM, Sánchez P, Gasol JM, Sánchez O, Ferrera I. A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs. MICROBIAL ECOLOGY 2023; 86:2161-2172. [PMID: 37148309 PMCID: PMC10497671 DOI: 10.1007/s00248-023-02220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.
| | - Ana María Cabello
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain.
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2
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Yang P, Zhu X, Ning K. Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship. Commun Biol 2023; 6:391. [PMID: 37037946 PMCID: PMC10085995 DOI: 10.1038/s42003-023-04753-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023] Open
Abstract
Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China.
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Tanabe Y, Yamaguchi H, Yoshida M, Kai A, Okazaki Y. Characterization of a bloom-associated alphaproteobacterial lineage, 'Candidatus Phycosocius': insights into freshwater algal-bacterial interactions. ISME COMMUNICATIONS 2023; 3:20. [PMID: 36906708 PMCID: PMC10008586 DOI: 10.1038/s43705-023-00228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/13/2023]
Abstract
Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage 'Candidatus Phycosocius' (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: 'Ca. Phycosocius spiralis.' Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5-3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in 'Ca. P. spiralis' that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.
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Affiliation(s)
- Yuuhiko Tanabe
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan.
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan.
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, 305-8506, Japan
| | - Masaki Yoshida
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Atsushi Kai
- Algae Biomass and Energy System R&D Center, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
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Villena‐Alemany C, Mujakić I, Porcal P, Koblížek M, Piwosz K. Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:60-71. [PMID: 36507772 PMCID: PMC10103773 DOI: 10.1111/1758-2229.13131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/19/2022] [Indexed: 05/20/2023]
Abstract
Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.
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Affiliation(s)
- Cristian Villena‐Alemany
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Petr Porcal
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
- Department of Hydrochemistry and Ecosystem Modelling, Biology Centre of the Czech Academy of SciencesInstitute of HydrobiologyČeské BudějoviceCzechia
| | - Michal Koblížek
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine EcologyNational Marine Fisheries Research InstituteGdyniaPoland
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Factors Affecting the Natural Regeneration of the Larix principis-rupprechtii Mayr Plantations: Evidence from the Composition and Co-Occurrence Network Structure of Soil Bacterial Communities. Processes (Basel) 2022. [DOI: 10.3390/pr10091771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacterial communities living in the soil can affect forests natural regeneration, but the effects of their composition and network inference on regeneration of Larix principis-rupprechtii Mayr plantations remain largely elusive. Therefore, the redundancy analysis and structure equations modeling of affecting elements for the regeneration of L. principis-rupprechtii plots including the diversity, composition and network structure of soil bacteria, topographic factors, light factors, and soil physicochemical properties have been conducted. It was found that the increased modularity of the soil bacterial community co-occurrence network and the enrichment of metabolic pathway bacteria had a significant positive effect on the successful regeneration (total effect of 0.84). The complexity of the soil bacterial community gradually decreased with the increase of stand regeneration, and the composition and structure of the flora became simpler (with standard path coefficients: −0.70). In addition, altitude also had a positive effect on regeneration with a total effect of 0.39. Soil nutrients had significantly negative effects on regeneration with total effects of −0.87. Soil bacterial communities may mediate the effects of soil nutrients, altitude, litter thickness, and herbaceous diversity on regeneration in L. principis-rupprechtii plantations. The results provide a great contribution to our understanding of regeneration-soil bacterial community interactions and the basis and important data for sustainable management of L. principis-rupprechtii plantations in the Lvliang Mountains located in northern China.
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Hoeger AL, Jehmlich N, Kipping L, Griehl C, Noll M. Associated bacterial microbiome responds opportunistic once algal host Scenedesmus vacuolatus is attacked by endoparasite Amoeboaphelidium protococcarum. Sci Rep 2022; 12:13187. [PMID: 35915148 PMCID: PMC9343445 DOI: 10.1038/s41598-022-17114-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
The interactions of microalgae and their associated microbiomes have come to the fore of applied phycological research in recent years. However, the functional mechanisms of microalgal interactions remain largely unknown. Here, we examine functional protein patterns of the microalgae Scenedesmus vacuolatus and its associated bacterial community during algal infection by the endoparasite Amoeboaphelidium protococcarum. We performed metaproteomics analyses of non-infected (NI) and aphelid-infected (AI) S.vacuolatus cultures to investigate underlying functional and physiological changes under infectious conditions. We observed an increase in bacterial protein abundance as well as a severe shift of bacterial functional patterns throughout aphelid-infection in comparison to NI treatment. Most of the bacterial proteins (about 55%) upregulated in AI were linked to metabolism and transport of amino acids, lipids, coenzymes, nucleotides and carbohydrates and to energy production. Several proteins associated with pathogenic bacterial-plant interactions showed higher protein abundance levels in AI treatment. These functional shifts indicate that associated bacteria involved in commensalistic or mutualistic interactions in NI switch to opportunistic lifestyles and facilitate pathogenic or saprotrophic traits in AI treatment. In summary, the native bacterial microbiome adapted its metabolism to algal host die off and is able to metabolize nutrients from injured cells or decompose dead cellular material.
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Affiliation(s)
- Anna-Lena Hoeger
- Competence Center Algae Biotechnology, Anhalt University of Applied Sciences, Koethen, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Permoserstr. 15, 04318, Leipzig, Germany
| | - Lydia Kipping
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Permoserstr. 15, 04318, Leipzig, Germany
| | - Carola Griehl
- Competence Center Algae Biotechnology, Anhalt University of Applied Sciences, Koethen, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany. .,Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
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Weigel BL, Miranda KK, Fogarty EC, Watson AR, Pfister CA. Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes. mSystems 2022; 7:e0142221. [PMID: 35642511 PMCID: PMC9238374 DOI: 10.1128/msystems.01422-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.
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Affiliation(s)
- Brooke L. Weigel
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
| | | | - Emily C. Fogarty
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Andrea R. Watson
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Catherine A. Pfister
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
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Suleiman M, Pennekamp F, Choffat Y, Petchey OL. Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem. Ecol Evol 2022; 12:e8793. [PMID: 35414897 PMCID: PMC8986512 DOI: 10.1002/ece3.8793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light‐dependent oxic–anoxic micro‐ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivation. Continuous measurements of oxygen concentration were made and a time series of full‐length 16S rRNA sequencing was used to quantify changes in alpha‐ and beta diversity. In the upper oxic layer, oxygen concentration decreased significantly under light reduction, but showed resilience in daily mean, minimum, and maximum after light conditions were restored to control level. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha diversity of the upper oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient in the longer term. In contrast, alpha diversity of the anoxic lower layer communities increased during the light reduction, but was resilient in the longer term. Community composition changed significantly during light reduction, and showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha diversity and the amplitude of daily oxygen fluctuations within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function (oxygen respiration) and structure, hence focusing on a single stability component could potentially be misleading.
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Affiliation(s)
- Marcel Suleiman
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Frank Pennekamp
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Yves Choffat
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Owen L. Petchey
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
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9
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Suleiman M, Pennekamp F, Choffat Y, Petchey OL. Contrasting resistance and resilience to light variation of the coupled oxic and anoxic components of an experimental microbial ecosystem. Ecol Evol 2022. [PMID: 35414897 DOI: 10.1101/2021.08.13.456201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Understanding how microbial communities of aquatic ecosystems respond to environmental change remains a critical challenge in microbial ecology. In this study, we used light-dependent oxic-anoxic micro-ecosystems to understand how the functioning and diversity of aerobic and anaerobic lake analog communities are affected by a pulse light deprivation. Continuous measurements of oxygen concentration were made and a time series of full-length 16S rRNA sequencing was used to quantify changes in alpha- and beta diversity. In the upper oxic layer, oxygen concentration decreased significantly under light reduction, but showed resilience in daily mean, minimum, and maximum after light conditions were restored to control level. Only the amplitude of diurnal fluctuations in oxygen concentrations did not recover fully, and instead tended to remain lower in treated ecosystems. Alpha diversity of the upper oxic layer communities showed a delayed increase after light conditions were restored, and was not resilient in the longer term. In contrast, alpha diversity of the anoxic lower layer communities increased during the light reduction, but was resilient in the longer term. Community composition changed significantly during light reduction, and showed resilience in the oxic layer and lack of resilience in the anoxic layer. Alpha diversity and the amplitude of daily oxygen fluctuations within and among treatments were strongly correlated, suggesting that higher diversity could lead to less variable oxygen concentrations, or vice versa. Our experiment showed that light deprivation induces multifaceted responses of community function (oxygen respiration) and structure, hence focusing on a single stability component could potentially be misleading.
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Affiliation(s)
- Marcel Suleiman
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Frank Pennekamp
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Yves Choffat
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | - Owen L Petchey
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
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Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls. mSystems 2021; 6:e0093421. [PMID: 34581594 PMCID: PMC8547455 DOI: 10.1128/msystems.00934-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day−1, with the highest rates (>4 day−1) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique. IMPORTANCE Growth is one of the main manifestations of life. It is assumed generally that bacterial growth is constrained mostly by nutrient availability (bottom-up control) and grazing (top-down control). Since marine bacteria represent a very diverse assembly of species with different metabolic properties, their growth characteristics also largely differ accordingly. Currently, the growth of marine microorganisms is typically evaluated using microscopy in combination with fluorescence in situ hybridization (FISH). However, these laborious techniques are limited in their throughput and taxonomical resolution. Therefore, we combined a classical manipulation experiment with next-generation sequencing to resolve the growth dynamics of almost 300 bacterial phylogroups in the coastal Adriatic Sea. The analysis documented that most of the phylogroups responded positively to both grazer removal and phosphate addition. We observed significant differences in growth kinetics among closely related species, which could not be distinguished by the classical FISH technique.
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11
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Galachyants AD, Krasnopeev AY, Podlesnaya GV, Potapov SA, Sukhanova EV, Tikhonova IV, Zimens EA, Kabilov MR, Zhuchenko NA, Gorshkova AS, Suslova MY, Belykh OI. Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal. Microorganisms 2021; 9:842. [PMID: 33920057 PMCID: PMC8071047 DOI: 10.3390/microorganisms9040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.
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Affiliation(s)
- Agnia Dmitrievna Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Andrey Yurjevich Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Galina Vladimirovna Podlesnaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Elena Viktorovna Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Irina Vasiljevna Tikhonova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Ekaterina Andreevna Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Marsel Rasimovich Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia Albertovna Zhuchenko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Anna Sergeevna Gorshkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
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Baquiran JIP, Nada MAL, Campos CLD, Sayco SLG, Cabaitan PC, Rosenberg Y, Ayalon I, Levy O, Conaco C. The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution. Microorganisms 2020; 8:E1566. [PMID: 33053643 PMCID: PMC7601249 DOI: 10.3390/microorganisms8101566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
Corals harbor a great diversity of symbiotic microorganisms that play pivotal roles in host nutrition, reproduction, and development. Changes in the ocean environment, such as increasing exposure to artificial light at night (ALAN), may alter these relationships and result in a decline in coral health. In this study, we examined the microbiome associated with gravid specimens of the reef-building coral Acropora digitifera. We also assessed the temporal effects of ALAN on the coral-associated microbial community using high-throughput sequencing of the 16S rRNA gene V4 hypervariable region. The A. digitifera microbial community was dominated by phyla Proteobacteria, Firmicutes, and Bacteroidetes. Exposure to ALAN had no large-scale effect on the coral microbiome, although taxa affiliated with Rhodobacteraceae, Caulobacteraceae, Burkholderiaceae, Lachnospiraceae, and Ruminococcaceae were significantly enriched in corals subjected to ALAN. We further noted an increase in the relative abundance of the family Endozoicomonadaceae (Endozoicomonas) as the spawning period approached, regardless of light treatment. These findings highlight the stability of the A. digitifera microbial community under short-term artificial light pollution and provide initial insights into the response of the collective holobiont to ALAN.
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Affiliation(s)
- Jake Ivan P. Baquiran
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Michael Angelou L. Nada
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Celine Luisa D. Campos
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Sherry Lyn G. Sayco
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Patrick C. Cabaitan
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
| | - Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
| | - Inbal Ayalon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
- Israel The H. Steinitz Marine Biology Laboratory, The Interuniversity Institute for Marine Sciences of Eilat, P.O. Box 469, Eilat 88103, Israel
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 39040, Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.R.); (I.A.); (O.L.)
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Quezon City 1101, Philippines; (J.I.P.B.); (M.A.L.N.); (C.L.D.C.); (S.L.G.S.); (P.C.C.)
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