1
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Silva-Solar S, Viver T, Wang Y, Orellana LH, Knittel K, Amann R. Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential. Syst Appl Microbiol 2024; 47:126555. [PMID: 39342656 DOI: 10.1016/j.syapm.2024.126555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 09/18/2024] [Accepted: 09/20/2024] [Indexed: 10/01/2024]
Abstract
Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class Acidimicrobiia, within the phylum Actinomycetota, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available Acidimicrobiia genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class Acidimicrobiia and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of Actinomycetota 16S rRNA gene sequences, and 3-7% of Bacteria. We propose Benthobacter isfjordensis gen. nov., sp. nov., Hadalibacter litoralis gen. nov., sp. nov., and two new species from Ilumatobacter, following SeqCode guidelines. In addition, we report the first in situ quantification of the family Ilumatobacteraceae, revealing its substantial presence (1-6%) in coastal sediments. This work highlights the need of refining the taxonomy of Acidimicrobiia to better understand their ecological contributions.
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Affiliation(s)
- Sebastián Silva-Solar
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany
| | - Tomeu Viver
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany
| | - Yueqing Wang
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsius Str 1, 28359 Bremen, Germany.
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2
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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3
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Kalenborn S, Zühlke D, Reintjes G, Riedel K, Amann RI, Harder J. Genes for laminarin degradation are dispersed in the genomes of particle-associated Maribacter species. Front Microbiol 2024; 15:1393588. [PMID: 39188312 PMCID: PMC11345257 DOI: 10.3389/fmicb.2024.1393588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/17/2024] [Indexed: 08/28/2024] Open
Abstract
Laminarin is a cytosolic storage polysaccharide of phytoplankton and macroalgae and accounts for over 10% of the world's annually fixed carbon dioxide. Algal disruption, for example, by viral lysis releases laminarin. The soluble sugar is rapidly utilized by free-living planktonic bacteria, in which sugar transporters and the degrading enzymes are frequently encoded in polysaccharide utilization loci. The annotation of flavobacterial genomes failed to identify canonical laminarin utilization loci in several particle-associated bacteria, in particular in strains of Maribacter. In this study, we report in vivo utilization of laminarin by Maribacter forsetii accompanied by additional cell growth and proliferation. Laminarin utilization coincided with the induction of an extracellular endo-laminarinase, SusC/D outer membrane oligosaccharide transporters, and a periplasmic glycosyl hydrolase family 3 protein. An ABC transport system and sugar kinases were expressed. Endo-laminarinase activity was also observed in Maribacter sp. MAR_2009_72, Maribacter sp. Hel_I_7, and Maribacter dokdonensis MAR_2009_60. Maribacter dokdonensis MAR_2009_71 lacked the large endo-laminarinase gene in the genome and had no endo-laminarinase activity. In all genomes, genes of induced proteins were scattered across the genome rather than clustered in a laminarin utilization locus. These observations revealed that the Maribacter strains investigated in this study participate in laminarin utilization, but in contrast to many free-living bacteria, there is no co-localization of genes encoding the enzymatic machinery for laminarin utilization.
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Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Greta Reintjes
- Microbial Carbohydrate Interaction Group, Department of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Rudolf I. Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [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: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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5
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Zhang T, Wang W, Leng Y, Huang Y, Xiong W, Chang F. Bacterial Diversity and Vertical Distribution Patterns in Sandy Sediments: A Study on the Bacterial Community Structure Based on Environmental Factors in Tributaries of the Yangtze River. Microorganisms 2024; 12:1178. [PMID: 38930560 PMCID: PMC11205631 DOI: 10.3390/microorganisms12061178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is known about the relationship between biogeochemistry processes and vertical spatial distribution of bacterial communities in sandy sediments. In this study, we used fluorescence quantitative PCR, high-throughput sequencing technology and statistical analysis to explore the vertical distribution pattern of bacterial community diversity and its influencing factors in sandy sediments of the Yangtze River Basin. The aim is to enrich the understanding of the ecological characteristics and functions of bacteria in river ecosystems. The results showed that both sediment bacterial abundance and diversity showed a gradual decrease from surface to bottom in the vertical distribution. The main environmental factors that influenced the bacterial distribution pattern were pore water dissolved oxygen (DO), total nitrogen (TN) concentration and sediment nitrogen (N) content. The dominant bacterial species, Massilia and Flavobacterium, are suitable for growth and reproduction in high oxygen and nutrient-richer environments, while Limnobacter prefers low oxygen or anaerobic conditions. The vertical distribution pattern of bacteria and its influencing factors in river sandy sediment found in this study differ from the results in mud sediment, which may be related to the larger granular gap between sandy sediment and the lower content of organic matter. The findings of this study further our understanding of the distribution patterns and ecological preferences of microbial communities in river sediments, providing insights into how these communities may adapt to varying environmental conditions.
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Affiliation(s)
- Tian Zhang
- Department of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (T.Z.); (Y.L.); (Y.H.); (W.X.)
- Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China;
| | - Weibo Wang
- Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China;
| | - Yifei Leng
- Department of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (T.Z.); (Y.L.); (Y.H.); (W.X.)
- Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes, Hubei University of Technology, Wuhan 430068, China
- Key Laboratory of Intelligent Health Perception and Ecological Restoration of Rivers and Lakes, Ministry of Education, Hubei University of Technology, Wuhan 430068, China
| | - Yu Huang
- Department of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (T.Z.); (Y.L.); (Y.H.); (W.X.)
- Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes, Hubei University of Technology, Wuhan 430068, China
- Key Laboratory of Intelligent Health Perception and Ecological Restoration of Rivers and Lakes, Ministry of Education, Hubei University of Technology, Wuhan 430068, China
| | - Wen Xiong
- Department of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (T.Z.); (Y.L.); (Y.H.); (W.X.)
- Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes, Hubei University of Technology, Wuhan 430068, China
- Key Laboratory of Intelligent Health Perception and Ecological Restoration of Rivers and Lakes, Ministry of Education, Hubei University of Technology, Wuhan 430068, China
| | - Fengyi Chang
- Department of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China; (T.Z.); (Y.L.); (Y.H.); (W.X.)
- Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes, Hubei University of Technology, Wuhan 430068, China
- Key Laboratory of Intelligent Health Perception and Ecological Restoration of Rivers and Lakes, Ministry of Education, Hubei University of Technology, Wuhan 430068, China
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6
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Kalenborn S, Zühlke D, Riedel K, Amann RI, Harder J. Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72. FEMS Microbiol Ecol 2024; 100:fiae045. [PMID: 38569650 PMCID: PMC11036162 DOI: 10.1093/femsec/fiae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.
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Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
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7
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Banchi E, Corre E, Del Negro P, Celussi M, Malfatti F. Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:126-142. [PMID: 38433960 PMCID: PMC10902248 DOI: 10.1007/s42995-023-00192-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 03/05/2024]
Abstract
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00192-z.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Erwan Corre
- FR2424, Station Biologique de Roscoff, Plateforme ABiMS (Analysis and Bioinformatics for Marine Science), Sorbonne Université CNRS, 29680 Roscoff, France
| | - Paola Del Negro
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
| | - Francesca Malfatti
- National Institute of Oceanography and Applied Geophysics OGS, Trieste, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
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8
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Moncada C, Arnosti C, Brüwer JD, de Beer D, Amann R, Knittel K. Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments. THE ISME JOURNAL 2024; 18:wrae159. [PMID: 39115410 PMCID: PMC11368169 DOI: 10.1093/ismejo/wrae159] [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: 06/06/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.
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Affiliation(s)
- Chyrene Moncada
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jan D Brüwer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Dirk de Beer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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9
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Copeland R, Zhang C, Hammer BK, Yunker PJ. Spatial constraints and stochastic seeding subvert microbial arms race. PLoS Comput Biol 2024; 20:e1011807. [PMID: 38277405 PMCID: PMC10849242 DOI: 10.1371/journal.pcbi.1011807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/07/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024] Open
Abstract
Surface attached communities of microbes grow in a wide variety of environments. Often, the size of these microbial community is constrained by their physical surroundings. However, little is known about how size constraints of a colony impact the outcome of microbial competitions. Here, we use individual-based models to simulate contact killing between two bacterial strains with different killing rates in a wide range of community sizes. We found that community size has a substantial impact on outcomes; in fact, in some competitions the identity of the most fit strain differs in large and small environments. Specifically, when at a numerical disadvantage, the strain with the slow killing rate is more successful in smaller environments than in large environments. The improved performance in small spaces comes from finite size effects; stochastic fluctuations in the initial relative abundance of each strain in small environments lead to dramatically different outcomes. However, when the slow killing strain has a numerical advantage, it performs better in large spaces than in small spaces, where stochastic fluctuations now aid the fast killing strain in small communities. Finally, we experimentally validate these results by confining contact killing strains of Vibrio cholerae in transmission electron microscopy grids. The outcomes of these experiments are consistent with our simulations. When rare, the slow killing strain does better in small environments; when common, the slow killing strain does better in large environments. Together, this work demonstrates that finite size effects can substantially modify antagonistic competitions, suggesting that colony size may, at least in part, subvert the microbial arms race.
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Affiliation(s)
- Raymond Copeland
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christopher Zhang
- Interdisciplinary Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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10
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Bonthond G, Beermann J, Gutow L, Neumann A, Barboza FR, Desiderato A, Fofonova V, Helber SB, Khodami S, Kraan C, Neumann H, Rohde S, Schupp PJ. Benthic microbial biogeographic trends in the North Sea are shaped by an interplay of environmental drivers and bottom trawling effort. ISME COMMUNICATIONS 2023; 3:132. [PMID: 38102238 PMCID: PMC10724143 DOI: 10.1038/s43705-023-00336-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Microbial composition and diversity in marine sediments are shaped by environmental, biological, and anthropogenic processes operating at different scales. However, our understanding of benthic microbial biogeography remains limited. Here, we used 16S rDNA amplicon sequencing to characterize benthic microbiota in the North Sea from the top centimeter of 339 sediment samples. We utilized spatially explicit statistical models, to disentangle the effects of the different predictors, including bottom trawling intensity, a prevalent industrial fishing practice which heavily impacts benthic ecosystems. Fitted models demonstrate how the geographic interplay of different environmental and anthropogenic drivers shapes the diversity, structure and potential metabolism of benthic microbial communities. Sediment properties were the primary determinants, with diversity increasing with sediment permeability but also with mud content, highlighting different underlying processes. Additionally, diversity and structure varied with total organic matter content, temperature, bottom shear stress and bottom trawling. Changes in diversity associated with bottom trawling intensity were accompanied by shifts in predicted energy metabolism. Specifically, with increasing trawling intensity, we observed a transition toward more aerobic heterotrophic and less denitrifying predicted metabolism. Our findings provide first insights into benthic microbial biogeographic patterns on a large spatial scale and illustrate how anthropogenic activity such as bottom trawling may influence the distribution and abundances of microbes and potential metabolism at macroecological scales.
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Affiliation(s)
- Guido Bonthond
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany.
| | - Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Lars Gutow
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | | | | | - Andrea Desiderato
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Department of Invertebrate Zoology and Hydrobiology, University of Lodz, 90-136, Lodz, Poland
| | - Vera Fofonova
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Stephanie B Helber
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Sahar Khodami
- Senckenberg am Meer Wilhelmshaven, German Centre for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
| | - Casper Kraan
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Hermann Neumann
- Thünen Institute of Sea Fisheries, Herwigstraße 31, 27572, Bremerhaven, Germany
| | - Sven Rohde
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129, Oldenburg, Germany
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11
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Wang M, Zhao K, Li X, Xie BB. Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains. Front Microbiol 2023; 14:1308767. [PMID: 38098661 PMCID: PMC10719935 DOI: 10.3389/fmicb.2023.1308767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear. Methods The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology. Results The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential. Discussion This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.
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Affiliation(s)
| | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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12
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VanMensel D, Chaganti SR, Droppo IG, Weisener CG. Microbe-sediment interactions in Great Lakes recreational waters: Implications for human health risk. Environ Microbiol 2023; 25:1605-1623. [PMID: 36998158 DOI: 10.1111/1462-2920.16378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
Abstract
Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.
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Affiliation(s)
- Danielle VanMensel
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, N9B 3P4, Windsor, Ontario, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, 4840 South State Street, Ann Arbor, Michigan, 48108, USA
| | - Ian G Droppo
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, N9B 3P4, Windsor, Ontario, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Avenue, N9B 3P4, Windsor, Ontario, Canada
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13
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Ferguson DK, Li C, Chakraborty A, Gittins DA, Fowler M, Webb J, Campbell C, Morrison N, MacDonald A, Hubert CRJ. Multi-year seabed environmental baseline in deep-sea offshore oil prospective areas established using microbial biodiversity. MARINE POLLUTION BULLETIN 2023; 194:115308. [PMID: 37517246 DOI: 10.1016/j.marpolbul.2023.115308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023]
Abstract
Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial microbial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along the Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar in space and time, with members of the family Woeseiaceae detected consistently in >1 % relative abundance, similar to seabed sediments in other parts of the world. Anomalous biodiversity results at one site featured lower Woeseiaceae as well as higher levels of bacterial groups specifically associated with cold seeps such as Aminicenantes. This was unexpected given that site selection was based on sediment geochemistry not revealing any petroleum hydrocarbons in these locations. This finding highlights the sensitivity and specificity of microbial DNA sequencing in environmental monitoring. Microbiome assessments like this one represent an important strategy for incorporating microbial biodiversity as a new and useful metric for establishing robust environmental baselines that are necessary for understanding ecosystem responses to marine pollution.
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Affiliation(s)
- Deidra K Ferguson
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Daniel A Gittins
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Martin Fowler
- Applied Petroleum Technology Canada, Calgary, Alberta, Canada
| | - Jamie Webb
- Applied Petroleum Technology Canada, Calgary, Alberta, Canada
| | - Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Nova Scotia, Canada
| | - Natasha Morrison
- Nova Scotia Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Nova Scotia, Canada
| | - Adam MacDonald
- Nova Scotia Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Nova Scotia, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Gomez MG, Muchongwe ST, Graddy CMR. Biomediated control of colloidal silica grouting using microbial fermentation. Sci Rep 2023; 13:14184. [PMID: 37648736 PMCID: PMC10468516 DOI: 10.1038/s41598-023-41402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
Colloidal silica grouting is a ground improvement technique capable of stabilizing weak problematic soils and achieving large reductions in soil hydraulic conductivities for applications including earthquake-induced liquefaction mitigation and groundwater flow control. In the conventional approach, chemical accelerants are added to colloidal silica suspensions that are introduced into soils targeted for improvement and the formation of a semi-solid silica gel occurs over time at a rate controlled by suspension chemistry and in situ geochemical conditions. Although the process has been extensively investigated, controlling the rate of gel formation in the presence of varying subsurface conditions and the limited ability of conventional methods to effectively monitor the gel formation process has posed practical challenges. In this study, a biomediated soil improvement process is proposed which utilizes enriched fermentative microorganisms to control the gelation of colloidal silica grouts through solution pH reductions and ionic strength increases. Four series of batch experiments were performed to investigate the ability of glucose fermenting microorganisms to be enriched in natural sands to induce geochemical changes capable of mediating silica gel formation and assess the effect of treatment solution composition on pH reduction behaviors. Complementary batch and soil column experiments were subsequently performed to upscale the process and explore the effectiveness of chemical, hydraulic, and geophysical methods to monitor microbial activity, gel formation, and engineering improvements. Results demonstrate that fermentative microorganisms can be successfully enriched and mediate gel formation in suspensions that would otherwise remain highly stable, thereby forgoing the need for chemical accelerants, increasing the reliability and control of colloidal silica grouting, enabling new monitoring approaches, and affording engineering enhancements comparable to conventional colloidal silica grouts.
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Affiliation(s)
- Michael G Gomez
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Samantha T Muchongwe
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Charles M R Graddy
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
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15
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Galván V, Pascutti F, Sandoval NE, Lanfranconi MP, Lozada M, Arabolaza AL, Mac Cormack WP, Alvarez HM, Gramajo HC, Dionisi HM. High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments. PLoS One 2023; 18:e0288509. [PMID: 37459319 PMCID: PMC10351704 DOI: 10.1371/journal.pone.0288509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.
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Affiliation(s)
- Virginia Galván
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Federico Pascutti
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Natalia E. Sandoval
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana P. Lanfranconi
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana Lozada
- Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), Puerto Madryn, Chubut, Argentina
| | - Ana L. Arabolaza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Walter P. Mac Cormack
- Instituto de Nanobiotecnología (NANOBIOTEC-UBA-CONICET), San Martín, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Antártico Argentino (IAA), San Martín, Buenos Aires, Argentina
| | - Héctor M. Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Hugo C. Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Hebe M. Dionisi
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Chubut, Argentina
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16
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Dionisi HM, Lozada M, Campos E. Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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17
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Bourceau OM, Ferdelman T, Lavik G, Mussmann M, Kuypers MMM, Marchant HK. Simultaneous sulfate and nitrate reduction in coastal sediments. ISME COMMUNICATIONS 2023; 3:17. [PMID: 36882570 PMCID: PMC9992702 DOI: 10.1038/s43705-023-00222-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.
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Affiliation(s)
- O M Bourceau
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - T Ferdelman
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - G Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - M Mussmann
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, A-1030, Vienna, Austria
| | - M M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - H K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany.
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18
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Srivastava A, Verma D. Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:752-772. [PMID: 35904740 DOI: 10.1007/s11356-022-22198-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V3-V4). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.
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Affiliation(s)
- Ankita Srivastava
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025
| | - Digvijay Verma
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India, 226025.
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The mud-dwelling clam Meretrix petechialis secretes endogenously synthesized erythromycin. Proc Natl Acad Sci U S A 2022; 119:e2214150119. [PMID: 36442100 PMCID: PMC9894158 DOI: 10.1073/pnas.2214150119] [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: 11/29/2022] Open
Abstract
Although lacking an adaptive immune system and often living in habitats with dense and diverse bacterial populations, marine invertebrates thrive in the presence of potentially challenging microbial pathogens. However, the mechanisms underlying this resistance remain largely unexplored and promise to reveal novel strategies of microbial resistance. Here, we provide evidence that a mud-dwelling clam, Meretrix petechialis, synthesizes, stores, and secretes the antibiotic erythromycin. Liquid chromatography coupled with mass spectrometry, immunocytochemistry, fluorescence in situ hybridization, RNA interference, and enzyme-linked immunosorbent assay revealed that this potent macrolide antimicrobial, thought to be synthesized only by microorganisms, is produced by specific mucus-rich cells beneath the clam's mantle epithelium, which interfaces directly with the bacteria-rich environment. The antibacterial activity was confirmed by bacteriostatic assay. Genetic, ontogenetic, phylogenetic and genomic evidence, including genotypic segregation ratios in a family of full siblings, gene expression in clam larvae, phylogenetic tree, and synteny conservation in the related genome region further revealed that the genes responsible for erythromycin production are of animal origin. The detection of this antibiotic in another clam species showed that the production of this macrolide is not exclusive to M. petechialis and may be a common strategy among marine invertebrates. The finding of erythromycin production by a marine invertebrate offers a striking example of convergent evolution in secondary metabolite synthesis between the animal and bacterial domains. These findings open the possibility of engineering-animal tissues for the localized production of an antibacterial secondary metabolite.
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20
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Influence of Nutrients and the Native Community on E. coli Survival in the Beach Environment. Appl Environ Microbiol 2022; 88:e0104322. [PMID: 36218359 PMCID: PMC9642020 DOI: 10.1128/aem.01043-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous research has identified E. coli populations that persist in freshwater beach sand distinct from fecal pollution events. This work identifies factors that influence the survival of E. coli in sand using laboratory microcosms to replicate beach conditions. Microcosms were deployed to examine the effect of genetic background, competition with native microbial community, and increased nutrient concentrations on E. coli survival. Survival was comparable between the phylotypes B1 and B2, however, deficiency of stress response greatly reduced survival. In the absence of the native community under nutrient conditions comparable to those observed in sand, E. coli cell densities remained within an order of magnitude of initial concentrations after 5 weeks of incubation. Increased nitrogen was associated with decreased decay rates in the first 2 weeks, and increased carbon appeared to provide an advantage at later time points. However, the highest survival was found with the addition of both carbon and nitrogen. Native sand seeded with fresh Cladophora maintained higher concentrations of E. coli, compared to sand containing decayed Cladophora or no Cladophora. Our findings demonstrate persistent E. coli populations in sand can be affected by the availability of carbon and nitrogen, the ability to regulate stress, and the presence of algal mats (i.e., Cladophora). Further, this work suggests that the native microbial communities may modulate survival by outcompeting E. coli for nutrients. IMPORTANCE Current monitoring for fecal pollution does not account for persistent E. coli populations in freshwater sand, which can result in higher concentrations in water when no threat to human health is present. This work examined the drivers for persistent E. coli populations in sand to aid beach management techniques. We examined the influence of nutrients, including localized sources such as stranded Cladophora, on E. coli populations. We found the major determinant of E. coli survival in freshwater beach sand was the addition of nutrients, specifically carbon and nitrogen concentrations 10-fold higher than baseline concentrations on beaches. This work provides the framework for identifying pollution sources that can promote E. coli survival in sand through the characterization of carbon and nitrogen content, which can be incorporated into beach management techniques. Through this improved knowledge, we can begin to understand E. coli fluctuations in water due to resuspension from sand into water.
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Wang K, Pan R, Fei H, Tong Q, Han F. Changes in soil prokaryotic communities and nitrogen cycling functions along a groundwater table drawdown gradient in desert wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156868. [PMID: 35752234 DOI: 10.1016/j.scitotenv.2022.156868] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Desert wetlands are evolving into deserts by groundwater table (GWT) drawdown. However, the changes in microbial communities and functions during the GWT drawdown are unclear, which hinders the predictive power of biogeochemical processes across the desertification. Here, 16S rRNA gene sequencing, PICRUSt2 and qPCR were used to investigate soil prokaryotic diversity, composition and nitrogen cycling gene abundance at four vegetation types [flooded swamp (FS), drained swamp (DS), desert grassland (DG), and bare sandy land (BS)] along a GWT decline gradient in the Mu Us Desert, northern China. Results showed that prokaryotic Shannon and Chao1 indexes were significantly reduced at BS than those at FS (p < 0.05). Whereas no significant difference was observed between FS, DS and DG (p > 0.05). Distinct shifts in community composition were found along the GWT decline gradient. The dominant taxa gradually changed from obligate anaerobes and eutrophic microbes to facultative anaerobes, and finally to aerobic, oligotrophic and drought-tolerant microbes. Soil moisture was the most important factor in regulating the communities. In addition, GWT drawdown inhibited the relative abundance of genes involved in nitrogen fixation, assimilatory nitrite reduction, and nitrate oxidation, but enhanced the relative abundance of genes related to denitrification, assimilated nitrate reduction, ammonia oxidation and ammonification. Thus, GWT drawdown inhibits nitrogen input potential and exacerbates nitrogen loss potential. These results help in understanding the succession characteristics of desert wetland desertification.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ruopeng Pan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Hongyan Fei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Qian Tong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Fengpeng Han
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China; Research Center on Soil & Water Conservation, Institute of Soil and Water Conservation, Chinese Academy of Sciences Ministry of Water Resources, Yangling, Shaanxi Province 712100, PR China.
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22
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Perliński P, Mudryk ZJ, Zdanowicz M, Kubera Ł. Abundance of Live and Dead Bacteriopsammon Inhabiting Sandy Ecosystems of Recreational Marine Beaches of the Southern Baltic Sea. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02079-5. [PMID: 35876854 DOI: 10.1007/s00248-022-02079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The study was carried out on four non-tidal sandy marine beaches located on the Polish part of the southern Baltic Sea coast. We applied a LIVE/DEAD™ BacLight™ Bacterial Viability Kit (Invitrogen™) method to determine the abundance of live and dead bacteriopsammon. Live psammon bacteria cells constituted 31-53% of the total number of bacteria inhabiting sand of the studied beaches. Abundance of live and dead psammon bacteria generally differed along the horizontal profile in all beaches. The maximum density of bacteria was noted in the dune and the middle part of the beach (dry zones) and the minimum in wet zones, i.e., under seawater surface and at the swash zone. Generally along the vertical profile, the highest numbers of two studied bacterial groups were noted in the surface sand layer, while with increasing sediment depth their numbers significantly decreased. The abundance of live and dead bacteria showed a distinct seasonal variation.
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Affiliation(s)
- Piotr Perliński
- Department of Experimental Biology, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Arciszewskiego 22B str, 76-200, Słupsk, Poland.
| | - Zbigniew Jan Mudryk
- Department of Experimental Biology, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Arciszewskiego 22B str, 76-200, Słupsk, Poland
| | - Marta Zdanowicz
- Department of Experimental Biology, Institute of Biology and Earth Sciences, Pomeranian University in Słupsk, Arciszewskiego 22B str, 76-200, Słupsk, Poland
| | - Łukasz Kubera
- Department of Microbiology and Immunobiology, Faculty of Biological Sciences, Kazimierz Wielki University, Al. Powstańców Wielkopolskich 10, 85-090, Bydgoszcz, Poland
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dos Santos JDN, João SA, Martín J, Vicente F, Reyes F, Lage OM. iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments. Microorganisms 2022; 10:1471. [PMID: 35889190 PMCID: PMC9319460 DOI: 10.3390/microorganisms10071471] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an "one strain many compounds" approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.
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Affiliation(s)
- José Diogo Neves dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Susana Afonso João
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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24
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Chen L, Zhao B, Palomo A, Sun Y, Cheng Z, Zhang M, Xia Y. Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations. WATER RESEARCH 2022; 220:118640. [PMID: 35661503 DOI: 10.1016/j.watres.2022.118640] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300-500 µm) and micron-scale (70-100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%-79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.
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Affiliation(s)
- Liming Chen
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Alejandro Palomo
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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25
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Okamoto N, Keeling PJ, Leander BS, Tai V. Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location. Mol Ecol 2022; 31:3210-3227. [PMID: 35364623 DOI: 10.1111/mec.16453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The microbial communities of sandy beaches are poorly described despite the biogeochemical importance and ubiquity of these ecosystems. Using metabarcoding of the 16S and 18S rRNA genes, we investigated the diversity, microhabitats (with or between sand grains), and intertidal distributions of microorganisms (including meiofauna) from pristine sandy beaches in British Columbia, Canada, and hypothesized that abiotic variations due to microhabitat or intertidal gradients influences the distribution of microorganisms on local scales. Bacterial, archaeal, and protistan communities of the sand were clearly distinct from interstitial communities, and from planktonic communities of the overlying seawater, which correlated with differences in function and lifestyle, e.g., sulfur reduction and gliding motility. In contrast, meiofaunal communities could not be distinguished by sample type, suggesting that they are more frequently mobilized between these microhabitats. Across intertidal zones, high intertidal, mid intertidal, and low intertidal/swash communities were distinct and correlated with moisture, organic carbon and phosphate content, implying that the distribution of microorganisms is influenced by intertidal abiotic gradients. However, few taxa at the genus or species level individually contributed to this zonation pattern; rather, a unique combination of multiple microbial taxa was more likely responsible. Although significant differences in microbial community composition on sandy beaches can be attributed to microhabitat and intertidal gradients, further investigations are needed to assess community assembly processes, the consistency of these distributions, and the functions of the majority of the microorganisms observed in the sand and their effects on the biogeochemistry and ecology of sandy beaches.
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Affiliation(s)
- Noriko Okamoto
- University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | | | - Brian S Leander
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Vera Tai
- University of British Columbia, Vancouver, British Columbia, Canada.,University of Western Ontario, London, Ontario, Canada
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26
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DNA- and RNA-based bacterial communities and geochemical zonation under changing sediment porewater dynamics on the Aldabra Atoll. Sci Rep 2022; 12:4257. [PMID: 35277525 PMCID: PMC8917147 DOI: 10.1038/s41598-022-07980-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022] Open
Abstract
The remote Aldabra Atoll, Seychelles, provides the rare opportunity to study bacterial communities in pristine carbonate sediments across an entire biome. The four sampled sites cover sand with high porewater exchange, bioturbated silt and mud with intermediate exchange, as well as a seasonally and episodically desiccated landlocked pool. As sediments harbour dead cells and environmental DNA alongside live cells, we used bacterial 16S rRNA gene and transcript analysis to distinguish between past and present inhabitants. Previously described laminated sediments mirroring past conditions in the Cerin, France could not be retrieved. Thus, the aim was adjusted to determine whether bacterial community composition and diversity follow typical geochemical zonation patterns at different locations of the atoll. Our data confirm previous observations that diversity decreases with depth. In the lagoon, the bacterial community composition changed from Pseudomonas dominating in the sand to diverse mixed surface and sulphate reduction zones in the anaerobic mud with strongly negative Eh. The latter correlated with high total alkalinity, ammonia, and total sulphide, alongside a decrease in SO42−/Cl− and high relative abundances of sulphate reducing (Halo-) Desulfovibrio, sulphur oxidizing Arcobacteraceae, photo(hetero)troph Cyanobacteria, Alphaproteobacteria, and fermenting Propionigenium. In contrast to expectations, deeper mud and pool sediments harboured high abundances of Halomonas or Alphaproteobacteria alongside high C/N and increased salinity. We believe that this atypical community shift may be driven by a change in the complexity of available organic matter.
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27
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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28
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Lee J, Hestrin R, Nuccio EE, Morrison KD, Ramon CE, Samo TJ, Pett-Ridge J, Ly SS, Laurence TA, Weber PK. Label-Free Multiphoton Imaging of Microbes in Root, Mineral, and Soil Matrices with Time-Gated Coherent Raman and Fluorescence Lifetime Imaging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1994-2008. [PMID: 35029104 DOI: 10.1021/acs.est.1c05818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging biogeochemical interactions in complex microbial systems─such as those at the soil-root interface─is crucial to studies of climate, agriculture, and environmental health but complicated by the three-dimensional (3D) juxtaposition of materials with a wide range of optical properties. We developed a label-free multiphoton nonlinear imaging approach to provide contrast and chemical information for soil microorganisms in roots and minerals with epi-illumination by simultaneously imaging two-photon excitation fluorescence (TPEF), coherent anti-Stokes Raman scattering (CARS), second-harmonic generation (SHG), and sum-frequency mixing (SFM). We used fluorescence lifetime imaging (FLIM) and time gating to correct CARS for the autofluorescence background native to soil particles and fungal hyphae (TG-CARS) using time-correlated single-photon counting (TCSPC). We combined TPEF, TG-CARS, and FLIM to maximize image contrast for live fungi and bacteria in roots and soil matrices without fluorescence labeling. Using this instrument, we imaged symbiotic arbuscular mycorrhizal fungi (AMF) structures within unstained plant roots in 3D to 60 μm depth. High-quality imaging was possible at up to 30 μm depth in a clay particle matrix and at 15 μm in complex soil preparation. TG-CARS allowed us to identify previously unknown lipid droplets in the symbiotic fungus, Serendipita bescii. We also visualized unstained putative bacteria associated with the roots of Brachypodium distachyon in a soil microcosm. Our results show that this multimodal approach holds significant promise for rhizosphere and soil science research.
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Affiliation(s)
- Janghyuk Lee
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rachel Hestrin
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Erin E Nuccio
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Keith D Morrison
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Christina E Ramon
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ty J Samo
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Life and Environmental Sciences Department, University of California Merced, Merced, California 95343, United States
| | - Sonny S Ly
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ted A Laurence
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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29
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Clark DR, McKew BA, Binley A, Heppell CM, Whitby C, Trimmer M. Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers. ISME COMMUNICATIONS 2022; 2:5. [PMID: 37938696 PMCID: PMC9723640 DOI: 10.1038/s43705-022-00087-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2023]
Abstract
Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.
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Affiliation(s)
- Dave R Clark
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.
- Institute for Analytics and Data Science, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK.
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Andrew Binley
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Catherine M Heppell
- School of Geography, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Corinne Whitby
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Mark Trimmer
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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30
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Demko AM, Patin NV, Jensen PR. Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques. Environ Microbiol 2021; 23:6859-6875. [PMID: 34636122 DOI: 10.1111/1462-2920.15798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 09/28/2021] [Indexed: 01/04/2023]
Abstract
The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.
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Affiliation(s)
- Alyssa M Demko
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Nastassia V Patin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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31
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Chen YJ, Leung PM, Wood JL, Bay SK, Hugenholtz P, Kessler AJ, Shelley G, Waite DW, Franks AE, Cook PLM, Greening C. Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. THE ISME JOURNAL 2021; 15:2986-3004. [PMID: 33941890 PMCID: PMC8443593 DOI: 10.1038/s41396-021-00988-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 02/03/2023]
Abstract
Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.
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Affiliation(s)
- Ya-Jou Chen
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Natural Resources Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Adam J Kessler
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia
- School of Earth, Atmosphere and Environment, Monash University, Clayton, VIC, Australia
| | - Guy Shelley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Perran L M Cook
- Water Studies Centre, School of Chemistry, Monash University, Clayton, VIC, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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32
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Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments. ISME JOURNAL 2021; 16:750-763. [PMID: 34584214 PMCID: PMC8857189 DOI: 10.1038/s41396-021-01111-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/04/2023]
Abstract
The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.
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33
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Eich A, Weber M, Lott C. Disintegration half-life of biodegradable plastic films on different marine beach sediments. PeerJ 2021; 9:e11981. [PMID: 34434671 PMCID: PMC8362673 DOI: 10.7717/peerj.11981] [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: 03/29/2021] [Accepted: 07/25/2021] [Indexed: 11/20/2022] Open
Abstract
The seafloor is considered the major sink for plastic debris in the world's oceans. Biodegradable polymers are available on the market as a substitute for conventional plastic and could potentially end up in the same environment. To gain more insight into the effects of different sediments on the degradation rate of biodegradable plastic we performed two iterative seawater tank experiments. First, to test the effect of sediment grain size, film of Mater-Bi HF03V, a blend of thermoplastic starch and biodegradable polyesters, was placed on the surface of mud as well as on four different grain size fractions of beach sand. Disintegration half-life was shortest on mud (139 days) and increased with the grain size of the beach sediment fractions (63-250 µm: 296 days; 250-500 µm: 310 days; 500-1,000 µm: 438 days; >1,000 µm: 428 days). We assume that the higher surface-to-volume ratio in fine sediment compared to coarse sediment led to a higher bacterial abundance and thus to faster disintegration rates. In a follow-up experiment, the <500 µm fraction of sediment from four different beaches around Isola d'Elba, Italy, was used to test plastic disintegration as above. Additionally, polyhydroxybutyrate (PHB, MIREL P5001) was used as a positive control and high-density polyethylene (HD-PE) as a negative control. No disintegration was observed for HD-PE. Mater-Bi HF03V and PHB disintegrated significantly differently on sediment from different sites, with half-lives of Mater-Bi HF03V ranging from 72 to 368 days and of PHB from 112 to 215 days. Here, the half-life was shortest on slightly coarser sediment and at potentially anthropogenically impacted sites. We assume that the effect of the grain size on the disintegration rate was masked by other parameters influencing the microbial community and activity. Understanding the parameters driving biodegradation is key to reliably report the range of disintegration rates occurring under the various conditions in different ecosystems.
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Wang W, Hu M, Shu X, Li H, Qi W, Yang Y, Zhang Q. Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146552. [PMID: 34030307 DOI: 10.1016/j.scitotenv.2021.146552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/06/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
The reservoir of microbial communities within the soil and the sediment performs many ecological functions and offers many ecosystem services. It has been suggested that its diversity and community structure could be explained by different grain size and heterogeneity. However, most of these conclusions come from studies conducted in terrestrial soil, impermeable marine and freshwater sediment (substrate). It remains to be seen whether these conclusions hold true in permeable substrate, especially in headwater river ecosystems. To address this, a field experiment was aimed to evaluate the link between grain median size and distribution heterogeneity and microbial diversity and community structure. Permeable substrate with gradient grain sizes and heterogeneities was inoculated in a headwater river in central China, while the diversity and community composition of the total microbial community and three denitrifier communities were investigated by high throughput sequencing three months later. The total microbial community was sequenced by 16S rRNA, a marker for taxonomic diversity. Three denitrifier communities were sequenced using three functional gene markers: nirK, nirS, and nosZ. The result showed that both the diversity and community structure of the total microbial community and three denitrifier communities were determined by water chemistry rather than grain size and size distribution heterogeneity, although grain size and heterogeneity positively influenced the nutrient concentrations of the substrate. Compared to the total microbial community, denitrification functional groups had more unique species proportions, indicating that functional genes were more sensitive to environmental change than the 16S rRNA gene. Our study fills a gap in understanding microbial communities in permeable sediment in a headwater river and highlights the less importance of grain size and heterogeneity on mm-scale in shaping the diversity and structure of microbiome.
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Affiliation(s)
- Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Mingming Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 10038, China
| | - Xiao Shu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenhua Qi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yuyi Yang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Quanfa Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
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Wolfsdorf G, Abrahão A, D'Angioli AM, de Sá Dechoum M, Meirelles ST, F. L. Pecoral L, Rowland L, da Silveira Verona L, B. Schmidt I, B. Sampaio A, S. Oliveira R. Inoculum origin and soil legacy can shape plant–soil feedback outcomes for tropical grassland restoration. Restor Ecol 2021. [DOI: 10.1111/rec.13455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gabriel Wolfsdorf
- Departamento de Biologia Vegetal Universidade Estadual de Campinas 6109 Campinas SP Brazil
- Programa de Pós‐Graduação em Ecologia Universidade Estadual de Campinas Campinas SP Brazil
| | - Anna Abrahão
- Programa de Pós‐Graduação em Biologia Vegetal Universidade Estadual de Campinas Campinas SP Brazil
- Department of Soil Biology Institute of Soil Science and Land Evaluation, University of Hohenheim 70599 Stuttgart Germany
| | - André M. D'Angioli
- Departamento de Biologia Vegetal Universidade Estadual de Campinas 6109 Campinas SP Brazil
- Programa de Pós‐Graduação em Ecologia Universidade Estadual de Campinas Campinas SP Brazil
| | - Michele de Sá Dechoum
- Department of Ecology and Zoology Federal University of Santa Catarina Florianópolis SC 88040‐900 Brazil
| | | | - Luísa F. L. Pecoral
- Departamento de Biologia Vegetal Universidade Estadual de Campinas 6109 Campinas SP Brazil
| | - Lucy Rowland
- College of Life and Environmental Sciences University of Exeter Exeter EX4 4RJ U.K
| | | | - Isabel B. Schmidt
- Ecology Department University of Brasília, Campus Universitário Darcy Ribeiro Brasília DF 70910‐900 Brazil
| | - Alexandre B. Sampaio
- Centro Nacional de Avaliação da Biodiversidade e de Pesquisa e Conservação do Cerrado Instituto Chico Mendes de Conservação da Biodiversidade—ICMBio Brasília DF Brazil
| | - Rafael S. Oliveira
- Departamento de Biologia Vegetal Universidade Estadual de Campinas 6109 Campinas SP Brazil
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Miksch S, Meiners M, Meyerdierks A, Probandt D, Wegener G, Titschack J, Jensen MA, Ellrott A, Amann R, Knittel K. Bacterial communities in temperate and polar coastal sands are seasonally stable. ISME COMMUNICATIONS 2021; 1:29. [PMID: 36739458 PMCID: PMC9723697 DOI: 10.1038/s43705-021-00028-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 04/18/2023]
Abstract
Coastal sands are biocatalytic filters for dissolved and particulate organic matter of marine and terrestrial origin, thus, acting as centers of organic matter transformation. At high temporal resolution, we accessed the variability of benthic bacterial communities over two annual cycles at Helgoland (North Sea), and compared it with seasonality of communities in Isfjorden (Svalbard, 78°N) sediments, where primary production does not occur during winter. Benthic community structure remained stable in both, temperate and polar sediments on the level of cell counts and 16S rRNA-based taxonomy. Actinobacteriota of uncultured Actinomarinales and Microtrichales were a major group, with 8 ± 1% of total reads (Helgoland) and 31 ± 6% (Svalbard). Their high activity (frequency of dividing cells 28%) and in situ cell numbers of >10% of total microbes in Svalbard sediments, suggest Actinomarinales and Microtrichales as key heterotrophs for carbon mineralization. Even though Helgoland and Svalbard sampling sites showed no phytodetritus-driven changes of the benthic bacterial community structure, they harbored significantly different communities (p < 0.0001, r = 0.963). The temporal stability of benthic bacterial communities is in stark contrast to the dynamic succession typical of coastal waters, suggesting that pelagic and benthic bacterial communities respond to phytoplankton productivity very differently.
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Affiliation(s)
| | - Mirja Meiners
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - David Probandt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Jürgen Titschack
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Senckenberg am Meer, Wilhelmshaven, Germany
| | - Maria A Jensen
- UNIS, The University Centre in Svalbard, Longyearbyen, Norway
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR. Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data. J Microbiol Methods 2021; 188:106271. [PMID: 34146605 DOI: 10.1016/j.mimet.2021.106271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 01/04/2023]
Abstract
Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. Quantitative estimates of the biomass of different taxonomic groups in samples were made through the analysis of PLFAs, and these were compared to the relative abundances of microbial taxa estimated from metabarcoding. Furthermore, we used the PLFA-based quantitative estimates of the biomass to adjust relative abundances of microbial groups determined by metabarcoding to provide insight into how the biomass of microbial taxa from PLFA analysis can improve understanding of microbial communities from environmental DNA samples. We used two sets of PLFA biomarkers that differed in their number of PLFAs to evaluate how PLFA biomarker selection influences biomass estimates. Metabarcoding and PLFA analysis provided significantly different views of bacterial composition, and these differences varied among substrates. We observed the most notable differences for the Gram-negative bacteria, which were overrepresented by metabarcoding in comparison to PLFA analysis. In contrast, the relative biomass and relative sequence abundances aligned reasonably well for Cyanobacteria across the tested freshwater substrates. Adjusting relative abundances of microbial taxa estimated by metabarcoding with PLFA-based quantification estimates of the microbial biomass led to significant changes in the microbial community compositions in all substrates. We recommend including independent estimates of the biomass of microbial groups to increase comparability among metabarcoding libraries from environmental samples, especially when comparing communities associated with different substrates.
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Affiliation(s)
- Natascha Lewe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Syrie Hermans
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Laura T Kelly
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Georgia Thomson-Laing
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Barbara Weisbrod
- Human and Environmental Toxicology, Department of Biology, Universität Konstanz, 78457 Konstanz, Germany
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street, East Nelson, 7010, New Zealand
| | - Robert A Keyzers
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Julie R Deslippe
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Centre for Biodiversity and Restoration Ecology, Victoria University of Wellington, Wellington 6012, New Zealand.
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Schutte CA, Huanca-Valenzuela P, Lavik G, Marchant HK, de Beer D. Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification. Front Microbiol 2021; 12:556268. [PMID: 34220727 PMCID: PMC8250833 DOI: 10.3389/fmicb.2021.556268] [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: 04/27/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.
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Affiliation(s)
- Charles A Schutte
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Gaute Lavik
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dirk de Beer
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Vaksmaa A, Knittel K, Abdala Asbun A, Goudriaan M, Ellrott A, Witte HJ, Vollmer I, Meirer F, Lott C, Weber M, Engelmann JC, Niemann H. Microbial Communities on Plastic Polymers in the Mediterranean Sea. Front Microbiol 2021; 12:673553. [PMID: 34220756 PMCID: PMC8243005 DOI: 10.3389/fmicb.2021.673553] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022] Open
Abstract
Plastic particles in the ocean are typically covered with microbial biofilms, but it remains unclear whether distinct microbial communities colonize different polymer types. In this study, we analyzed microbial communities forming biofilms on floating microplastics in a bay of the island of Elba in the Mediterranean Sea. Raman spectroscopy revealed that the plastic particles mainly comprised polyethylene (PE), polypropylene (PP), and polystyrene (PS) of which polyethylene and polypropylene particles were typically brittle and featured cracks. Fluorescence in situ hybridization and imaging by high-resolution microscopy revealed dense microbial biofilms on the polymer surfaces. Amplicon sequencing of the 16S rRNA gene showed that the bacterial communities on all plastic types consisted mainly of the orders Flavobacteriales, Rhodobacterales, Cytophagales, Rickettsiales, Alteromonadales, Chitinophagales, and Oceanospirillales. We found significant differences in the biofilm community composition on PE compared with PP and PS (on OTU and order level), which shows that different microbial communities colonize specific polymer types. Furthermore, the sequencing data also revealed a higher relative abundance of archaeal sequences on PS in comparison with PE or PP. We furthermore found a high occurrence, up to 17% of all sequences, of different hydrocarbon-degrading bacteria on all investigated plastic types. However, their functioning in the plastic-associated biofilm and potential role in plastic degradation needs further assessment.
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Affiliation(s)
- Annika Vaksmaa
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alejandro Abdala Asbun
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Maaike Goudriaan
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Andreas Ellrott
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Harry J Witte
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Ina Vollmer
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | - Florian Meirer
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, Netherlands
| | | | | | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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Jokanović S, Kajan K, Perović S, Ivanić M, Mačić V, Orlić S. Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116383. [PMID: 33387780 DOI: 10.1016/j.envpol.2020.116383] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.
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Affiliation(s)
- Sandra Jokanović
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Katarina Kajan
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia
| | - Svetlana Perović
- Faculty of Science and Mathematics, University of Montenegro, 81 000, Podgorica, Montenegro
| | - Maja Ivanić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10 000, Zagreb, Croatia
| | - Vesna Mačić
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia.
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Di Cesare A, Pjevac P, Eckert E, Curkov N, Miko Šparica M, Corno G, Orlić S. The role of metal contamination in shaping microbial communities in heavily polluted marine sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114823. [PMID: 32512474 DOI: 10.1016/j.envpol.2020.114823] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/25/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and abundance of metal and antibiotic resistance genes is sediments collected from the Pula Bay (Croatia), one of the most significantly polluted sites along the Croatian coast. With a collection of 14 samples from the bay area, we were able to generate a detailed status quo picture of a site that only recently started a cleaning and remediation process (closing of sewage pipes and reduction of industrial activity). The concentrations of heavy metals in Pula Bay sediments are significantly higher than in pristine sediments from the Adriatic Sea, and in some cases, manifold exceed international sediment quality guidelines. While the sedimentary concentrations of heavy metals did significantly influence the abundance of the tested metal resistance genes, no strong effect of heavy metal pollution on the overall microbial community composition was observed. Like in many other marine sediments, Gammaproteobacteria, Bacteroidota and Desulfobacterota dominated the microbial community composition in most samples, and community assembly was primarily driven by water column depth and nutrient (carbon and nitrogen) availability, regardless of the degree of heavy metal pollution.
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Affiliation(s)
- Andrea Di Cesare
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Petra Pjevac
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090, Vienna, Austria
| | - Ester Eckert
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Neven Curkov
- Ruđer Bošković Institute, Division for Marine and Environmental Research, Zagreb, Croatia
| | | | - Gianluca Corno
- MEG-Molecular Ecology Group, Water Research Institute, CNR-IRSA, Largo Tonolli 50, 28922, Verbania, Italy
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Material Chemistry, Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean Region, Microbial Ecology, Zagreb, Croatia.
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Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 2020; 15:e0234839. [PMID: 32853201 PMCID: PMC7451513 DOI: 10.1371/journal.pone.0234839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
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Affiliation(s)
- Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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Nascimento JR, Easson CG, Jurelevicius DDA, Lopez JV, Bidone ED, Sabadini-Santos E. Microbial community shift under exposure of dredged sediments from a eutrophic bay. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:539. [PMID: 32705349 DOI: 10.1007/s10661-020-08507-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities occur in almost every habitat. To evaluate the homeostasis disruption of in situ microbiomes, dredged sediments from Guanabara Bay-Brazil (GB) were mixed with sediments from outside of the bay (D) in three different proportions (25%, 50%, and 75%) which we called GBD25, GBD50, and GBD75. Grain size, TOC, and metals-as indicators of complex contamination-dehydrogenase (DHA) and esterase enzymes (EST)-as indicators of microbial community availability-were determined. Microbial community composition was addressed by amplifying the 16S rRNA gene for DGGE analysis and sequencing using MiSeq platform (Illumina).We applied the quality ratio index (QR) to the GB, D, and every GBD mixture to integrate geochemical parameters with our microbiome data. QR indicated high environmental risk for GB and every GBD mixture, and low risk for D. The community shifted from aerobic to anaerobic profile, consistent with the characteristics of GB. Sample D was dominated by JTB255 marine benthic group, related to low impacted areas. Milano-WF1B-44 was the most representative of GB, often found in anaerobic and sulfur enriched environments. In GBD, the denitrifying sulfur-oxidizing bacteria, Sulfurovum, was the most representative, typically found in suboxic or anoxic niches. The canonical correspondence analysis was able to explain 60% of the community composition variation and exhibit the decrease of environmental quality as the contamination increases. Physiological and taxonomic shifts of the microbial assemblage in sediments were inferred by QR, which was suitable to determine sediment risk. The study produced sufficient information to improve the dredging plan and management.
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Affiliation(s)
- Juliana R Nascimento
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil.
| | - Cole G Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
- Biology Department, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Diogo de A Jurelevicius
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21944-570, Brazil
| | - Jose V Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, 33004, USA
| | - Edison D Bidone
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
| | - Elisamara Sabadini-Santos
- Programa de Pós-Graduação em Geociências (Geoquímica), Instituto de Química, Universidade Federal Fluminense, Niterói, RJ, 24020-150, Brazil
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Nitschke MR, Fidalgo C, Simões J, Brandão C, Alves A, Serôdio J, Frommlet JC. Symbiolite formation: a powerful in vitro model to untangle the role of bacterial communities in the photosynthesis-induced formation of microbialites. THE ISME JOURNAL 2020; 14:1533-1546. [PMID: 32203119 PMCID: PMC7242451 DOI: 10.1038/s41396-020-0629-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 11/09/2022]
Abstract
Microbially induced calcification is an ancient, community-driven mineralisation process that produces different types of microbialites. Symbiolites are photosynthesis-induced microbialites, formed by calcifying co-cultures of dinoflagellates from the family Symbiodiniaceae and bacteria. Symbiolites encase the calcifying community as endolithic cells, pointing at an autoendolithic niche of symbiotic dinoflagellates, and provide a rare opportunity to study the role of bacteria in bacterial-algal calcification, as symbiodiniacean cultures display either distinct symbiolite-producing (SP) or non-symbiolite-producing (NP) phenotypes. Using Illumina sequencing, we found that the bacterial communities of SP and NP cultures differed significantly in the relative abundance of 23 genera, 14 families, and 2 phyla. SP cultures were rich in biofilm digesters from the phylum Planctomycetes and their predicted metagenomes were enriched in orthologs related to biofilm formation. In contrast, NP cultures were dominated by biofilm digesters from the Bacteroidetes, and were inferred as enriched in proteases and nucleases. Functional assays confirmed the potential of co-cultures and bacterial isolates to produce biofilms and point at acidic polysaccharides as key stimulators for mineral precipitation. Hence, bacteria appear to influence symbiolite formation primarily through their biofilm-producing and modifying activity and we anticipate that symbiolite formation, as a low-complexity in vitro model, will significantly advance our understanding of photosynthesis-induced microbial calcification processes.
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Affiliation(s)
- Matthew R Nitschke
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
- Climate Change Cluster, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Cátia Fidalgo
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João Simões
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Cláudio Brandão
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Artur Alves
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - João Serôdio
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jörg C Frommlet
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, University of Aveiro, 3810-193, Aveiro, Portugal.
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Moelling K, Broecker F. Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2020; 2020:1646943. [PMID: 32565838 PMCID: PMC7256708 DOI: 10.1155/2020/1646943] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022]
Abstract
Polluted air poses a significant threat to human health. Exposure to particulate matter (PM) and harmful gases contributes to cardiovascular and respiratory diseases, including allergies and obstructive lung disease. Air pollution may also be linked to cancer and reduced life expectancy. Uptake of PM has been shown to cause pathological changes in the intestinal microbiota in mice and humans. Less is known about the effects of pollution-associated microbiota on human health. Several recent studies described the microbiomes of urban and rural air samples, of the stratosphere and sand particles, which can be transported over long distances, as well as the air of indoor environments. Here, we summarize the current knowledge on airborne bacterial, viral, and fungal communities and discuss their potential consequences on human health. The current data suggest that bacterial pathogens are typically too sparse and short-lived in air to pose a significant risk for infecting healthy people. However, airborne fungal spores may exacerbate allergies and asthma. Little information is available on viruses including phages, and future studies are likely to detect known and novel viruses with a yet unknown impact on human health. Furthermore, varying experimental protocols have been employed in the recent microbiome and virome studies. Therefore, standardized methodologies will be required to allow for better comparisons between studies. Air pollution has been linked to more severe outcomes of SARS (severe acute respiratory syndrome) coronavirus (SARS-CoV) infections. This may have contributed to severe SARS-CoV-2 outbreaks, especially those in China, Northern Italy, Iran, and New York City.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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An BA, Kleinbub S, Ozcan O, Koerdt A. Iron to Gas: Versatile Multiport Flow-Column Revealed Extremely High Corrosion Potential by Methanogen-Induced Microbiologically Influenced Corrosion (Mi-MIC). Front Microbiol 2020; 11:527. [PMID: 32296410 PMCID: PMC7136402 DOI: 10.3389/fmicb.2020.00527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/11/2020] [Indexed: 01/01/2023] Open
Abstract
Currently, sulfate-reducing bacteria (SRB) is regarded as the main culprit of microbiologically influenced corrosion (MIC), mainly due to the low reported corrosion rates of other microorganisms. For example, the highest reported corrosion rate for methanogens is 0.065 mm/yr. However, by investigating methanogen-induced microbiologically influenced corrosion (Mi-MIC) using an in-house developed versatile multiport flow test column, extremely high corrosion rates were observed. We analyzed a large set of carbon steel beads, which were sectionally embedded into the test columns as substrates for iron-utilizing methanogen Methanobacterium IM1. After 14 days of operation using glass beads as fillers for section separation, the highest average corrosion rate of Methanobacterium IM1 was 0.2 mm/yr, which doubled that of Desulfovibrio ferrophilus IS5 and Desulfovibrio alaskensis 16109 investigated at the same conditions. At the most corroded region, nearly 80% of the beads lost 1% of their initial weight (fast-corrosion), resulting in an average corrosion rate of 0.2 mm/yr for Methanobacterium IM1-treated columns. When sand was used as filler material to mimic sediment conditions, average corrosion rates for Methanobacterium IM1 increased to 0.3 mm/yr (maximum 0.52 mm/yr) with over 83% of the beads having corrosion rates above 0.3 mm/yr. Scanning electron images of metal coupons extracted from the column showed methanogenic cells were clustered close to the metal surface. Methanobacterium IM1 is a hydrogenotrophic methanogen with higher affinity to metal than H2. Unlike SRB, Methanobacterium IM1 is not restricted to the availability of sulfate concentration in the environment. Thus, the use of the multiport flow column provided a new insight on the corrosion potential of methanogens, particularly in dynamic conditions, that offers new opportunities for monitoring and development of mitigation strategies. Overall, this study shows (1) under certain conditions methanogenic archaea can cause higher corrosion than SRB, (2) specific quantifications, i.e., maximum, average, and minimum corrosion rates can be determined, and (3) that spatial statistical evaluations of MIC can be carried out.
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Affiliation(s)
| | | | | | - Andrea Koerdt
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
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Ahmerkamp S, Marchant HK, Peng C, Probandt D, Littmann S, Kuypers MMM, Holtappels M. The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments. Sci Rep 2020; 10:3573. [PMID: 32107429 PMCID: PMC7046789 DOI: 10.1038/s41598-020-60557-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/13/2020] [Indexed: 11/08/2022] Open
Abstract
Sandy sediments cover 50-60% of the continental shelves and are highly efficient bioreactors in which organic carbon is remineralized and inorganic nitrogen is reduced to N2. As such they seem to play an important role, buffering the open ocean from anthropogenic nitrogen inputs and likely remineralizing the vast amounts of organic matter formed in the highly productive surface waters. To date however, little is known about the interrelation between porewater transport, grain properties and microbial colonization and the consequences for remineralization rates in sandy sediments. To constrain the effect of theses factors on remineralization in silicate sands, we incubated North Sea sediments in flow-through reactors after separating into five different grain size fractions. Bulk sediment and sediment grain properties were measured along with microbial colonization and cell abundances, oxygen consumption and denitrification rates. Volumetric oxygen consumption ranged from 14 to 77 µmol O2 l-1 h-1 while nitrogen-loss via denitrification was between 3.7 and 8.4 µmol N l-1 h-1. Oxygen consumption and denitrification rates were linearly correlated to the microbial cell abundances, which ranged from 2.9 to 5.4·108 cells cm-3. We found, that cell abundance and consumption rates in sandy sediments are influenced (i) by the surface area available for microbial colonization and (ii) by the exposure of these surfaces to the solute-supplying porewater flow. While protective structures such as cracks and depressions promote microbial colonization, the oxygen demand is only met by good ventilation of these structures, which is supported by a high sphericity of the grains. Based on our results, spherical sand grains with small depressions, i.e. golf ball like structures, provide the optimal supporting mineral structure for microorganisms on continental shelves.
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Affiliation(s)
- Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany.
- Marum Center for Marine Environmental Sciences, Bremen, Germany.
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Chao Peng
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
- University Tübingen, Center for Applied Geoscience, Geomicrobiology, Geschwister-Scholl-Platz, 72074, Tübingen, Germany
| | - David Probandt
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
- Marum Center for Marine Environmental Sciences, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
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Taylor HB, Kurtz HD. Microbial community structure shows differing levels of temporal stability in intertidal beach sands of the grand strand region of South Carolina. PLoS One 2020; 15:e0229387. [PMID: 32106250 PMCID: PMC7046189 DOI: 10.1371/journal.pone.0229387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Studies of microbial community structure in intertidal and supratidal beach sands along the California and Gulf of Mexico coasts have begun to reveal geographical patterns in microbial diversity through the use of next generation sequencing technology. Only a few studies have targeted communities along the Eastern seaboard, leaving a variety of microbial ecosystems uncharacterized. In this study, we examine the microbial community structure within three South Carolina beaches along the Grand Strand via sequencing of the V4 region of the 16S rRNA gene to discern relationships between diversity and temporal or regional factors. Gammaproteobacteria, Planctomycetes, Acidobacteria, and Actinobacteria dominated the composition of these beaches. Diversity analyses revealed that highly diverse communities were similar in overall composition and diversity but showed different levels of community structure stability over time. The community structure in Pawleys Island sands showed no significant change over time, while Garden City experienced significant shifts between each sampling date. Community structure also differed between beaches and, to a lesser degree, sampling date. These data provide evidence of the high microbial diversity within these beach sands and suggest that even though beaches of the same geographic region can show similarity in composition and diversity at a particular timepoint, the nature of their community structure and underlying diversity may differ comparatively and over time.
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Affiliation(s)
- Harrison B. Taylor
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Harry D. Kurtz
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
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Centler F, Günnigmann S, Fetzer I, Wendeberg A. Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining. Microorganisms 2020; 8:microorganisms8020190. [PMID: 32019172 PMCID: PMC7074749 DOI: 10.3390/microorganisms8020190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 01/03/2023] Open
Abstract
Natural microbial communities in soils are highly diverse, allowing for rich networks of microbial interactions to unfold. Identifying key players in these networks is difficult as the distribution of microbial diversity at the local scale is typically non-uniform, and is the outcome of both abiotic environmental factors and microbial interactions. Here, using spatially resolved microbial presence-absence data along an aquifer transect contaminated with hydrocarbons, we combined co-occurrence analysis with association rule mining to identify potential keystone species along the hydrocarbon degradation process. Derived co-occurrence networks were found to be of a modular structure, with modules being associated with specific spatial locations and metabolic activity along the contamination plume. Association rules identify species that never occur without another, hence identifying potential one-sided cross-feeding relationships. We find that hub nodes in the rule network appearing in many rules as targets qualify as potential keystone species that catalyze critical transformation steps and are able to interact with varying partners. By contrasting analysis based on data derived from bulk samples and individual soil particles, we highlight the importance of spatial sample resolution. While individual inferred interactions are hypothetical in nature, requiring experimental verification, the observed global network patterns provide a unique first glimpse at the complex interaction networks at work in the microbial world.
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Affiliation(s)
- Florian Centler
- Department of Environmental Microbiology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany (A.W.)
- Correspondence: ; Tel.: +49-341-235-1336
| | - Sarah Günnigmann
- Department of Environmental Microbiology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany (A.W.)
| | - Ingo Fetzer
- Stockholm Resilience Centre, Stockholm University, Kräftriket 2B, 11419 Stockholm, Sweden
| | - Annelie Wendeberg
- Department of Environmental Microbiology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany (A.W.)
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50
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Flemming HC, Wuertz S. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol 2020; 17:247-260. [PMID: 30760902 DOI: 10.1038/s41579-019-0158-9] [Citation(s) in RCA: 719] [Impact Index Per Article: 179.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.
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Affiliation(s)
- Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Singapore, Singapore. .,Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Singapore, Singapore. .,School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore.
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