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Dickey JR, Swenie RA, Turner SC, Winfrey CC, Yaffar D, Padukone A, Beals KK, Sheldon KS, Kivlin SN. The Utility of Macroecological Rules for Microbial Biogeography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.
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Sathicq MB, Unrein F, Gómez N. Recurrent pattern of picophytoplankton dynamics in estuaries around the world: The case of Río de la Plata. MARINE ENVIRONMENTAL RESEARCH 2020; 161:105136. [PMID: 32971494 DOI: 10.1016/j.marenvres.2020.105136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
The picoplankton is an important component of aquatic food webs and plays a significant biogeochemical and ecological role in the environment. Little is known about this fraction of the plankton in temperate estuaries and especially in South America. In this article, we study the absolute and relative importance of the picoplankton along an annual cycle, and their relationship with physical and chemical variables in the Río de la Plata estuary. We also review the existing research in estuaries around the world concerning this community and present our results in a global context. The seasonal variation in the abundance of the different groups analyzed was very noticeable. Phycocyanin-rich picocyanobacteria (Pcy) were the main component (in abundance and in biovolume) of the picophytoplankton (PPP) almost during the whole year, with a maximum abundance of 7.3 × 105 cell mL-1 in summer, three orders of magnitude higher compared to autumn-winter. Picoeukaryotes, larger phytoplankton and heterotrophic bacteria showed the same seasonal trend, although with a lower range of variation than that of the Pcy. Considering all the phototrophic planktonic fractions, in terms of biomass, the PPP reached a maximum of 43% of the total biomass in spring. The dynamics of PPP found in this area are consistent with the observed in other temperate estuaries, where temperature is the main variable that influences its development, and with a high seasonal variation. Additionally, the absolute and relative importance of Pcy showed a consistently increasing trend towards lower latitude estuaries. The review also showed us that there is scarce information related to the picoplankton fraction in the Southern Hemisphere, its sanitary implications due to their potential of toxicity or their ecological role in coastal zones. The results presented here show the importance of this fraction, not only in Río de la Plata, but in many estuaries of the world, with a clear increase of relative abundance as we approach the equator.
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Affiliation(s)
- María Belén Sathicq
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) UNLP-CONICET, Buenos Aires, Argentina; Istituto di Ricerca Sulle Acque (IRSA) CNR, Verbania, Italy.
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Argentina
| | - Nora Gómez
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) UNLP-CONICET, Buenos Aires, Argentina
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Coutinho FH, Thompson CC, Cabral AS, Paranhos R, Dutilh BE, Thompson FL. Modelling the influence of environmental parameters over marine planktonic microbial communities using artificial neural networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 677:205-214. [PMID: 31059870 DOI: 10.1016/j.scitotenv.2019.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 05/13/2023]
Abstract
Guanabara Bay is a tropical estuarine ecosystem that receives massive anthropogenic impacts from the metropolitan region of Rio de Janeiro. This ecosystem suffers from an ongoing eutrophication process that has been shown to promote the emergence of potentially pathogenic bacteria, giving rise to public health concerns. Although previous studies have investigated how environmental parameters influence the microbial community of Guanabara Bay, they often have been limited to small spatial and temporal gradients and have not been integrated into predictive mathematical models. Our objective was to fill this knowledge gap by building models that could predict how temperature, salinity, phosphorus, nitrogen and transparency work together to regulate the abundance of bacteria, chlorophyll and Vibrio (a potential human pathogen) in Guanabara Bay. To that end, we built artificial neural networks to model the associations between these variables. These networks were carefully validated to ensure that they could provide accurate predictions without biases or overfitting. The estimated models displayed high predictive capacity (Pearson correlation coefficients ≥0.67 and root mean square error ≤ 0.55). Our findings showed that temperature and salinity were often the most important factors regulating the abundance of bacteria, chlorophyll and Vibrio (absolute importance ≥5) and that each of these has a unique level of dependence on nitrogen and phosphorus for their growth. These models allowed us to estimate the Guanabara Bay microbiome's response to changes in environmental conditions, which allowed us to propose strategies for the management and remediation of Guanabara Bay.
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Affiliation(s)
- F H Coutinho
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, the Netherlands; Utrecht University, Theorethical Biology and Bioinformatics, Utrecht, the Netherlands.
| | - C C Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - A S Cabral
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - R Paranhos
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil
| | - B E Dutilh
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen, the Netherlands; Utrecht University, Theorethical Biology and Bioinformatics, Utrecht, the Netherlands
| | - F L Thompson
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia (IB), Rio de Janeiro, Brazil; Universidade Federal do Rio de Janeiro (UFRJ), COPPE, SAGE, Rio de Janeiro, Brazil.
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Behera P, Mahapatra S, Mohapatra M, Kim JY, Adhya TK, Raina V, Suar M, Pattnaik AK, Rastogi G. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 595:472-485. [PMID: 28395262 DOI: 10.1016/j.scitotenv.2017.03.271] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Sofia Mahapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, 46241 Busan, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Vishakha Raina
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India.
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Zozaya-Valdés E, Roth-Schulze AJ, Thomas T. Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community. Front Microbiol 2016; 7:161. [PMID: 26925036 PMCID: PMC4757742 DOI: 10.3389/fmicb.2016.00161] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/01/2016] [Indexed: 01/08/2023] Open
Abstract
In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga's chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.
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Affiliation(s)
| | | | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, SydneyNSW, Australia
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Pavloudi C, Oulas A, Vasileiadou K, Sarropoulou E, Kotoulas G, Arvanitidis C. Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea). Mar Genomics 2016; 28:71-81. [PMID: 26831186 DOI: 10.1016/j.margen.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/25/2016] [Accepted: 01/25/2016] [Indexed: 11/27/2022]
Abstract
Lagoons are naturally enriched habitats, with unstable environmental conditions caused by their confinement, shallow depth and state of saprobity. The frequent fluctuations of the abiotic variables cause severe changes in the abundance and distribution of biota. This relationship has been studied extensively for the macrofaunal communities, but not sufficiently so for the bacterial ones. The aim of the present study was to explore the biodiversity patterns of bacterial assemblages and to examine whether these patterns are associated with biogeographic and environmental factors. For this purpose, sediment samples were collected from five lagoons located in the Amvrakikos Gulf (Ionian Sea, Western Greece). DNA was extracted from the sediment and was further processed through 16S rRNA pyrosequencing. The results of this exploratory study imply that salinity is the environmental factor best correlated with the bacterial community pattern, which has also been suggested in similar studies but for macrofaunal community patterns. In addition, the bacterial community of the brackish lagoons is differentiated from that of the brackish-marine lagoons. The findings of this study indicate that the studied lagoons have distinct bacterial communities.
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Affiliation(s)
- Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece; Biology Department, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece; Department of Microbial Ecophysiology, Faculty of Biology, University of Bremen, 28359, Bremen, Germany; Department of Biology, Faculty of Sciences, University of Ghent, 9000 Ghent, Belgium.
| | - Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Katerina Vasileiadou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Thalassocosmos, P.O. Box 2214, 71003 Heraklion, Crete, Greece.
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Gregoracci GB, Soares ACDS, Miranda MD, Coutinho R, Thompson FL. Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition. PLoS One 2015; 10:e0137090. [PMID: 26327119 PMCID: PMC4556663 DOI: 10.1371/journal.pone.0137090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/22/2015] [Indexed: 11/18/2022] Open
Abstract
Although previous studies have described opposing states in upwelling regions, i.e., the rise of cold nutrient-rich waters and prevalence of surface warm nutrient-poor waters, few have addressed the transition from one state to the other. This study aimed to describe the microbial and viral structure during this transition and was able to obtain the taxonomic and metabolic compositions as well as physical-chemical data. This integrated approach allowed for a better understanding of the dynamics of the downwelling upwelling transition, suggesting that a wealth of metabolic processes and ecological interactions are occurring in the minute fractions of the plankton (femto, pico, nano). These processes and interactions included evidence of microbial predominance during downwelling (with nitrogen recycling and aerobic anoxygenic photosynthesis), different viral predation pressures over primary production in different states (cyanobacteria vs eukaryotes), and a predominance of diatoms and selected bacterial and archaeal groups during upwelling (with the occurrence of a wealth of nitrogen metabolism involving ammonia). Thus, the results provided insights into which microbes, viruses and microbial-mediated processes are probably important in the functioning of upwelling systems.
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Affiliation(s)
- Gustavo Bueno Gregoracci
- Departamento de Ciências do Mar, UNIFESP Baixada Santista. Santos, SP, Brazil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Milene Dias Miranda
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz (IOC)-FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo, RJ, Brazil
| | - Fabiano L. Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
- Laboratório de Sistemas Avançados de Gestão de Produção—SAGE—COPPE, Centro de Gestão Tecnológica—CT2, UFRJ, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Bacterial Diversity Associated with the Coccolithophorid Algae Emiliania huxleyi and Coccolithus pelagicus f. braarudii. BIOMED RESEARCH INTERNATIONAL 2015; 2015:194540. [PMID: 26273594 PMCID: PMC4529885 DOI: 10.1155/2015/194540] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/30/2015] [Indexed: 02/01/2023]
Abstract
Coccolithophores are unicellular calcifying marine phytoplankton that can form large and conspicuous blooms in the oceans and make significant contributions to oceanic carbon cycling and atmospheric CO2 regulation. Despite their importance, the bacterial diversity associated with these algae has not been explored for ecological or biotechnological reasons. Bacterial membership of Emiliania huxleyi and Coccolithus pelagicus f. braarudii cultures was assessed using cultivation and cultivation-independent methods. The communities were species rich compared to other phytoplankton cultures. Community analysis identified specific taxa which cooccur in all cultures (Marinobacter and Marivita). Hydrocarbon-degrading bacteria were found in all cultures. The presence of Acidobacteria, Acidimicrobidae, Schlegelella, and Thermomonas was unprecedented but were potentially explained by calcification associated with coccolith production. One strain of Acidobacteria was cultivated and is closely related to a marine Acidobacteria isolated from a sponge. From this assessment of the bacterial diversity of coccolithophores, a number of biotechnological opportunities are evident, from bioprospecting for novel taxa such as Acidobacteria to helping understand the relationship between obligate hydrocarbonoclastic bacteria occurrence with phytoplankton and to revealing bacterial taxa that have a specific association with algae and may be suitable candidates as a means to improve the efficiency of mass algal cultivation.
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Rodriguez-Mora MJ, Scranton MI, Taylor GT, Chistoserdov AY. The dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing. FEMS Microbiol Ecol 2015. [PMID: 26209697 DOI: 10.1093/femsec/fiv088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Massively parallel tag sequencing was applied to describe the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin. In total, 14 samples from the Cariaco Basin were collected over a period of eight years from two stations. A total of 244 357 unique bacterial V6 amplicons were sequenced. The total number of operational taxonomic units (OTUs) found in this study was 4692, with a range of 511-1491 OTUs per sample. Approximately 95% of the OTUs found in the redox transition zone and anoxic layers of Cariaco are represented by less than 50 amplicons suggesting that only about 5% of the bacterial OTUs are responsible for the bulk of the microbial processes in the basin redox transition and anoxic zones. The same dominant OTUs were observed across all eight years of sampling although periodic fluctuations in their proportion were apparent. No distinctive differences were observed between the bacterial communities from the redox transition and anoxic layers of the Cariaco Basin water column. The largest proportion of amplicons belongs to Gammaproteobacteria represented mostly by sulfide oxidizers, followed by Marine Group A (originally described as SAR406; Gordon and Giovannoni 1996), a group of uncultured bacteria hypothesized to be involved in metal reduction, and sulfate-reducing Deltaproteobacteria. Gammaproteobacteria, Deltaproteobacteria and Marine Group A make up 67-90% of all V6 amplicons sequenced in this study. This strongly suggests that the basin's microbial communities are actively involved in the sulfur-related metabolism and coupling of the sulfur and carbon cycles. According to detrended canonical correspondence analysis, ecological factors such as chemoautotrophy, nitrate and oxidized and reduced sulfur compounds influence the structuring and distribution of the Cariaco microbial communities.
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Affiliation(s)
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Andrei Y Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
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10
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Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights 2015; 9:75-88. [PMID: 25983555 PMCID: PMC4426941 DOI: 10.4137/bbi.s12462] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 12/14/2022] Open
Abstract
Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of "metagenomics", often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards.
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Affiliation(s)
- Anastasis Oulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
- Department of Biology, University of Ghent, Ghent, Belgium
- Department of Microbial Ecophysiology, University of Bremen, Bremen, Germany
| | - Paraskevi Polymenakou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Georgios A Pavlopoulos
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
| | - Nikolas Papanikolaou
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ioannis Iliopoulos
- Division of Basic Sciences, University of Crete, Medical School, Heraklion, Crete, Greece
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Gülay A, Smets BF. An improved method to set significance thresholds for β diversity testing in microbial community comparisons. Environ Microbiol 2014; 17:3154-67. [PMID: 25534614 DOI: 10.1111/1462-2920.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/11/2014] [Indexed: 02/01/2023]
Abstract
Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters.
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Affiliation(s)
- Arda Gülay
- Department of Environmental Engineering, Technical University of Denmark, Building 113, Miljøvej, 2800, Kongens Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Building 113, Miljøvej, 2800, Kongens Lyngby, Denmark
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12
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Yang RH, Wang XL, Su JH, Li Y, Jiang SP, Gu F, Yao YJ. Bacterial diversity in native habitats of the medicinal fungus Ophiocordyceps sinensis on Tibetan Plateau as determined using Illumina sequencing data. FEMS Microbiol Lett 2014; 362:fnu044. [PMID: 25743069 DOI: 10.1093/femsle/fnu044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ophiocordyceps sinensis is one of the most well-known traditional Chinese medicinal fungi. In this study, bacterial diversity in the soils of native habitats of O. sinensis was investigated using Illumina sequencing data. A total of 525,000 sequences of V6-16S rRNA were analyzed. The number of OTUs from each sample ranged from 13,858 to 15,978 at 97% sequence similarity cut-off. The results demonstrated that the deep sequencing approach provides improved access to rare genotypes. Richness indices and Shannon's diversity index did not differ significantly between samples collected from locations where O. sinensis was present (Os1-3) and not present (NOs1-3). Classified bacterial sequences were grouped into 23 phyla including Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, etc. The Venn diagram revealed that 7183 OTUs belonging to 14 phyla were shared by Os, NOs and MP (mycelial pellicle wrapping the sclerotium of O. sinensis) samples, possibly representing a core microbiome existing in native habitats of O. sinensis, and that 863 belonging to 12 phyla were shared by Os and MP samples, possibly related to the occurrence of O. sinensis. Overall, the results revealed a high bacterial diversity in the soil samples and the relationships between the bacterial diversity and O. sinensis merit further investigation.
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Affiliation(s)
- Rui-Heng Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Liang Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China
| | - Jin-He Su
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Ping Jiang
- ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China Tibet Plateau Institute of Biology, Lhasa 850001, China
| | - Fei Gu
- Institute of Animal Science, Aba Academy of Science and Technology, Wenchuan 623000, China
| | - Yi-Jian Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China ITPB-IMCAS Key Joint Laboratory of Alpine Fungi, Lhasa 850001, China
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Alonso C, Piccini C, Unrein F, Bertoglio F, Conde D, Pernthaler J. Environmental dynamics as a structuring factor for microbial carbon utilization in a subtropical coastal lagoon. Front Microbiol 2013; 4:14. [PMID: 23423262 PMCID: PMC3573325 DOI: 10.3389/fmicb.2013.00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 01/20/2013] [Indexed: 11/20/2022] Open
Abstract
Laguna de Rocha belongs to a series of shallow coastal lagoons located along South America. It is periodically connected to the sea through a sand bar, exhibiting a hydrological cycle where physicochemical and biological gradients are rapidly established and destroyed. Its most frequent state is the separation of a Northern zone with low salinity, high turbidity and nutrient load, and extensive macrophyte growth, and a Southern zone with higher salinity and light penetration, and low nutrient content and macrophyte biomass. This zonation is reflected in microbial assemblages with contrasting abundance, activity, and community composition. The physicochemical conditions exerted a strong influence on community composition, and transplanted assemblages rapidly transformed to resembling the community of the recipient environment. Moreover, the major bacterial groups responded differently to their passage between the zones, being either stimulated or inhibited by the environmental changes, and exhibiting contrasting sensitivities to gradients. Addition of allochthonous carbon sources induced pronounced shifts in the bacterial communities, which in turn affected the microbial trophic web by stimulating heterotrophic flagellates and virus production. By contrast, addition of organic and inorganic nutrient sources (P or N) did not have significant effects. Altogether, our results suggest that (i) the planktonic microbial assemblage of this lagoon is predominantly carbon-limited, (ii) different bacterial groups cope differently with this constraint, and (iii) the hydrological cycle of the lagoon plays a key role for the alleviation or aggravation of bacterial carbon limitation. Based on these findings we propose a model of how hydrology affects the composition of bacterioplankton and of carbon processing in Laguna de Rocha. This might serve as a starting hypothesis for further studies about the microbial ecology of this lagoon, and of comparable transitional systems.
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Affiliation(s)
- Cecilia Alonso
- Functional Ecology of Aquatic Systems, Centro Universitario Región Este, Universidad de la RepúblicaRocha, Uruguay
| | - Claudia Piccini
- Instituto de Investigaciones Biológicas Clemente EstableMontevideo, Uruguay
| | - Fernando Unrein
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional de San MartínBuenos Aires, Argentina
| | - Florencia Bertoglio
- Functional Ecology of Aquatic Systems, Centro Universitario Región Este, Universidad de la RepúblicaRocha, Uruguay
| | - Daniel Conde
- Facultad de Ciencias, Universidad de la RepúblicaMontevideo, Uruguay
| | - Jakob Pernthaler
- Limnological Station, Institute of Plant Biology, Zurich UniversityKilchberg, Switzerland
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14
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Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis. PLoS One 2012; 7:e39905. [PMID: 22768320 PMCID: PMC3388064 DOI: 10.1371/journal.pone.0039905] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/29/2012] [Indexed: 11/19/2022] Open
Abstract
The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.
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15
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Gregoracci GB, Nascimento JR, Cabral AS, Paranhos R, Valentin JL, Thompson CC, Thompson FL. Structuring of bacterioplankton diversity in a large tropical bay. PLoS One 2012; 7:e31408. [PMID: 22363639 PMCID: PMC3283626 DOI: 10.1371/journal.pone.0031408] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/10/2012] [Indexed: 12/05/2022] Open
Abstract
Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).
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Affiliation(s)
- Gustavo B. Gregoracci
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Juliana R. Nascimento
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Anderson S. Cabral
- Laboratory of Hydrobiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Rodolfo Paranhos
- Laboratory of Hydrobiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Jean L. Valentin
- Laboratory of Zooplankton, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane C. Thompson
- Laboratory of Molecular Genetics of Microorganisms, IOC-FIOCRUZ, Rio de Janeiro, Brazil
| | - Fabiano L. Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- * E-mail:
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16
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Bruce T, de Castro A, Kruger R, Thompson CC, Thompson FL. Microbial Diversity of Brazilian Biomes. ADVANCES IN MICROBIAL ECOLOGY 2012. [DOI: 10.1007/978-1-4614-2182-5_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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Ghiglione JF, Murray AE. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environ Microbiol 2011; 14:617-29. [PMID: 22003839 DOI: 10.1111/j.1462-2920.2011.02601.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Marine bacterioplankton studies over the annual cycle in polar systems are limited due to logistic constraints in site access and support. Here, we conducted a comparative study of marine bacterioplankton sampled at several time points over the annual cycle (12 occasions each) at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish a better understanding of the extent and nature of variation in diversity and community structure at these different latitudes (49-64S). Molecular methods targeting the 16S rRNA gene (DGGE, CE-SSCP and tag pyrosequencing) suggest a strong seasonal pattern with higher richness in winter and a clear influence of phytoplankton bloom events on bacterioplankton community structure and diversity in both locations. The distribution of sequence tags within Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions. At both sites, several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed intense seasonal variation often with similar trends at both sites. This enhanced understanding of variability in dominant groups of bacterioplankton over the annual cycle contributes to an expanding baseline to understand climate change impacts in the coastal zone of polar oceans and provides a foundation for comparison with open ocean polar systems.
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Affiliation(s)
- J F Ghiglione
- CNRS, UMR7621, Laboratoire d'Océanographie Microbienne LOMIC, F-66651 Banyuls-sur-Mer, France
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