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Piwosz K, Villena-Alemany C, Całkiewicz J, Mujakić I, Náhlík V, Dean J, Koblížek M. Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon. FEMS Microbiol Ecol 2024; 100:fiae090. [PMID: 38886127 PMCID: PMC11229431 DOI: 10.1093/femsec/fiae090] [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: 12/19/2023] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, 81-332 Gdynia, Poland
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Joanna Całkiewicz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, 81-332 Gdynia, Poland
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Vít Náhlík
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, University of South Bohemia, 389 25 České Budějovice, Czechia
| | - Jason Dean
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, 379 01 Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [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: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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Wang Y, Zou Q. Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences. MICROBIAL ECOLOGY 2024; 87:74. [PMID: 38771320 PMCID: PMC11108897 DOI: 10.1007/s00248-024-02390-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.
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Affiliation(s)
- Yansu Wang
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054, China.
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Stojan I, Šantić D, Villena-Alemany C, Trumbić Ž, Matić F, Vrdoljak Tomaš A, Lepen Pleić I, Piwosz K, Kušpilić G, Ninčević Gladan Ž, Šestanović S, Šolić M. Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network. ENVIRONMENTAL MICROBIOME 2024; 19:28. [PMID: 38685092 PMCID: PMC11059731 DOI: 10.1186/s40793-024-00573-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea. RESULTS Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton. CONCLUSION This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.
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Affiliation(s)
- Iva Stojan
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Danijela Šantić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia.
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Frano Matić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Ana Vrdoljak Tomaš
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Kasia Piwosz
- Department of Fisheries, Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Grozdan Kušpilić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | | | - Stefanija Šestanović
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Mladen Šolić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
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Koblížek M, Ferrera I, Kolářová E, Duhamel S, Popendorf KJ, Gasol JM, Van Mooy BAS. Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre. Appl Environ Microbiol 2024; 90:e0003224. [PMID: 38551354 PMCID: PMC11022572 DOI: 10.1128/aem.00032-24] [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: 01/08/2024] [Accepted: 03/08/2024] [Indexed: 04/18/2024] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.
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Affiliation(s)
- Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Eva Kolářová
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Science, Třeboň, Czechia
| | - Solange Duhamel
- Department of Cellular and Molecular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kimberly J. Popendorf
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Coral Gables, Florida, USA
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Benjamin A. S. Van Mooy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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Ratnawati SE, Kuuliala L, Verschuere N, Cnockaert M, Vandamme P, Devlieghere F. The exploration of dominant spoilage bacteria in blue mussels (Mytilus edulis) stored under different modified atmospheres by MALDI-TOF MS in combination with 16S rRNA sequencing. Food Microbiol 2024; 118:104407. [PMID: 38049269 DOI: 10.1016/j.fm.2023.104407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
Few studies have addressed species-level identification of spoilage bacteria in blue mussels packed under modified atmospheres (MAs). We investigated the effect of MAs and seasons on the tentative species-level of dominant spoilage bacteria in blue mussels. Summer (s) and winter (w) blue mussels were stored at 4 °C in the atmospheres (%CO2/O2/N2): A40s (30/40/30), B60s (40/60/0), C60s (0/60/40), A40w (30/40/30), and D75w (25/75/0). In total, 122 culturable isolates were obtained at the final stage of shelf life, when mortality was high (56-100%) and total psychrotrophic bacteria counted >7 log CFU g-1. Biochemical properties were analyzed using gram reactions, catalase and oxidase activities, and salt tolerance tests. Culturable isolates were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16 S rRNA gene sequence analysis. Spoilage potential tests were investigated by evaluating protease, lipase, and fermentation activities as well as gas and H2S production. The culturable isolates showed tolerance to varied salt concentrations. Psychromonas arctica, Pseudoalteromonas elyakovii, and Shewanella frigidimarina were dominating in specific MAs. Winter blue mussels resulted in a higher variation of spoilage bacteria, including S. frigidimarina, S. vesiculosa, S. polaris, Micrococcus luteus, Paeniglutamicibacter terrestris sp. nov., and Alteromonas sp.
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Affiliation(s)
- S E Ratnawati
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Department of Fisheries, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - L Kuuliala
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium; Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - N Verschuere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - M Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - P Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - F Devlieghere
- Research Unit Food Microbiology and Food Preservation (FMFP), Department of Food Technology, Safety and Health, Part of Food2Know, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Zhang Y, Liu J, Song D, Yao P, Zhu S, Zhou Y, Jin J, Zhang XH. Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater. WATER RESEARCH 2024; 248:120849. [PMID: 37979570 DOI: 10.1016/j.watres.2023.120849] [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: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.
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Affiliation(s)
- Yulin Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Derui Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Shaodong Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yi Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jian Jin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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8
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Gazulla CR, Cabello AM, Sánchez P, Gasol JM, Sánchez O, Ferrera I. A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs. MICROBIAL ECOLOGY 2023; 86:2161-2172. [PMID: 37148309 PMCID: PMC10497671 DOI: 10.1007/s00248-023-02220-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.
| | - Ana María Cabello
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain.
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9
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Rey-Velasco X, Deulofeu-Capo O, Sanz-Sáez I, Cardelús C, Ferrera I, Gasol JM, Sánchez O. Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability. Microbiol Spectr 2023; 11:e0089023. [PMID: 37747249 PMCID: PMC10580928 DOI: 10.1128/spectrum.00890-23] [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: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations. IMPORTANCE Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
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Affiliation(s)
| | - Ona Deulofeu-Capo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Sanz-Sáez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA-CSIC), Barcelona, Catalonia, Spain
| | - Clara Cardelús
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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10
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Ai D, Chen L, Xie J, Cheng L, Zhang F, Luan Y, Li Y, Hou S, Sun F, Xia LC. Identifying local associations in biological time series: algorithms, statistical significance, and applications. Brief Bioinform 2023; 24:bbad390. [PMID: 37930023 DOI: 10.1093/bib/bbad390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/21/2023] [Accepted: 09/14/2023] [Indexed: 11/07/2023] Open
Abstract
Local associations refer to spatial-temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.
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Affiliation(s)
- Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Lulu Chen
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiemin Xie
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Longwei Cheng
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083, China
| | - Fang Zhang
- Shenwan Hongyuan Securities Co. Ltd., Shanghai 200031, China
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan 250100, China
| | - Yang Li
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
| | - Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, California, 90007, USA
| | - Li Charlie Xia
- Department of Statistics and Financial Mathematics, School of Mathematics, South China University of Technology, Guangzhou 510641, China
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11
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Peng Q, Lin L, Tu Q, Wang X, Zhou Y, Chen J, Jiao N, Zhou J. Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates. mSystems 2023; 8:e0128322. [PMID: 37417747 PMCID: PMC10469889 DOI: 10.1128/msystems.01283-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/12/2023] [Indexed: 07/08/2023] Open
Abstract
Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.
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Affiliation(s)
- Qiannan Peng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaopeng Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Yueyue Zhou
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Jiyu Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Joint Lab for Ocean Research and Education at Shandong University, Xiamen University and Dalhousie University, Qingdao, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Oklahoma, USA
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, USA
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12
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Brennan GL, Logares R. Tracking contemporary microbial evolution in a changing ocean. Trends Microbiol 2023; 31:336-345. [PMID: 36244921 DOI: 10.1016/j.tim.2022.09.001] [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: 11/09/2021] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 10/16/2022]
Abstract
Ocean microbes are fundamental for the functioning of the Earth system. Yet, our understanding of how they are reacting to global change in terms of evolution is limited. Microbes typically grow in large populations and reproduce quickly, which may allow them to rapidly adapt to environmental stressors compared to larger organisms. However, genetic evidence of contemporary evolution in wild microbes is scarce. We must begin coordinated efforts to establish new microbial time-series and explore novel tools, experiments, and data to fill this knowledge gap. The development of coordinated microbial 'genomic' observatories will provide the unprecedented opportunity to track contemporary microbial evolution in the ocean and explore the role of evolution in enabling wild microbes to respond to global change.
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Affiliation(s)
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, 08003 Barcelona, Spain.
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13
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Bolaños LM, Tait K, Somerfield PJ, Parsons RJ, Giovannoni SJ, Smyth T, Temperton B. Influence of short and long term processes on SAR11 communities in open ocean and coastal systems. ISME COMMUNICATIONS 2022; 2:116. [PMID: 37938786 PMCID: PMC9723719 DOI: 10.1038/s43705-022-00198-1] [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: 07/04/2022] [Revised: 10/21/2022] [Accepted: 11/01/2022] [Indexed: 07/18/2023]
Abstract
SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.
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Affiliation(s)
- Luis M Bolaños
- School of Biosciences, University of Exeter, Exeter, UK.
| | - Karen Tait
- Plymouth Marine Laboratory, Plymouth, UK
| | | | | | | | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK.
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14
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Czech L, Stamatakis A, Dunthorn M, Barbera P. Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade. FRONTIERS IN BIOINFORMATICS 2022; 2:871393. [PMID: 36304302 PMCID: PMC9580882 DOI: 10.3389/fbinf.2022.871393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.
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Affiliation(s)
- Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
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15
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Krabberød AK, Deutschmann IM, Bjorbækmo MFM, Balagué V, Giner CR, Ferrera I, Garcés E, Massana R, Gasol JM, Logares R. Long-term patterns of an interconnected core marine microbiota. ENVIRONMENTAL MICROBIOME 2022; 17:22. [PMID: 35526063 PMCID: PMC9080219 DOI: 10.1186/s40793-022-00417-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/20/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ocean microbes constitute ~ 70% of the marine biomass, are responsible for ~ 50% of the Earth's primary production and are crucial for global biogeochemical cycles. Marine microbiotas include core taxa that are usually key for ecosystem function. Despite their importance, core marine microbes are relatively unknown, which reflects the lack of consensus on how to identify them. So far, most core microbiotas have been defined based on species occurrence and abundance. Yet, species interactions are also important to identify core microbes, as communities include interacting species. Here, we investigate interconnected bacteria and small protists of the core pelagic microbiota populating a long-term marine-coastal observatory in the Mediterranean Sea over a decade. RESULTS Core microbes were defined as those present in > 30% of the monthly samples over 10 years, with the strongest associations. The core microbiota included 259 Operational Taxonomic Units (OTUs) including 182 bacteria, 77 protists, and 1411 strong and mostly positive (~ 95%) associations. Core bacteria tended to be associated with other bacteria, while core protists tended to be associated with bacteria. The richness and abundance of core OTUs varied annually, decreasing in stratified warmers waters and increasing in colder mixed waters. Most core OTUs had a preference for one season, mostly winter, which featured subnetworks with the highest connectivity. Groups of highly associated taxa tended to include protists and bacteria with predominance in the same season, particularly winter. A group of 13 highly-connected hub-OTUs, with potentially important ecological roles dominated in winter and spring. Similarly, 18 connector OTUs with a low degree but high centrality were mostly associated with summer or autumn and may represent transitions between seasonal communities. CONCLUSIONS We found a relatively small and dynamic interconnected core microbiota in a model temperate marine-coastal site, with potential interactions being more deterministic in winter than in other seasons. These core microbes would be essential for the functioning of this ecosystem over the year. Other non-core taxa may also carry out important functions but would be redundant and non-essential. Our work contributes to the understanding of the dynamics and potential interactions of core microbes possibly sustaining ocean ecosystem function.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
| | - Ina M Deutschmann
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Marit F M Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway
| | - Vanessa Balagué
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Caterina R Giner
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Isabel Ferrera
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640, Fuengirola, Málaga, Spain
| | - Esther Garcés
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain
- Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, 0316, Oslo, Norway.
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Spain.
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16
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Gazulla CR, Auladell A, Ruiz-González C, Junger PC, Royo-Llonch M, Duarte CM, Gasol JM, Sánchez O, Ferrera I. Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans. Environ Microbiol 2022; 24:2222-2238. [PMID: 35084095 DOI: 10.1111/1462-2920.15835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/17/2021] [Accepted: 10/29/2021] [Indexed: 01/04/2023]
Abstract
The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.
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Affiliation(s)
- Carlota R Gazulla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain.,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Pedro C Junger
- Department of Hydrobiology (DHB), Laboratory of Microbial Processes and Biodiversity (LMPB), Universidade Federal de São Carlos (UFSCar), São Carlos, SP, 13565-905, Brazil
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, 08003, Spain.,Centre for Marine Ecosystems Research, School of Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya, 08193, Spain
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, 29640 Fuengirola, Málaga, Spain
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17
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Auladell A, Barberán A, Logares R, Garcés E, Gasol JM, Ferrera I. Seasonal niche differentiation among closely related marine bacteria. THE ISME JOURNAL 2022; 16:178-189. [PMID: 34285363 PMCID: PMC8692485 DOI: 10.1038/s41396-021-01053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
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Affiliation(s)
- Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Center for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Fuengirola, Málaga, Spain.
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18
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Lambert S, Lozano JC, Bouget FY, Galand PE. Seasonal marine microorganisms change neighbours under contrasting environmental conditions. Environ Microbiol 2021; 23:2592-2604. [PMID: 33760330 DOI: 10.1111/1462-2920.15482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/12/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023]
Abstract
Marine picoplankton contribute to global carbon sequestration and nutrient recycling. These processes are directly related to the composition of communities, which in turn depends on microbial interactions and environmental forcing. Under regular seasonal cycles, marine communities show strong predictable patterns of annual re-occurrences, but little is known about the effect of environmental perturbation on their organization. The aim of our study was to investigate the co-occurrence patterns of planktonic picoeukaryote, bacteria and archaea under contrasting environmental conditions. The study was designed to have high sampling frequency that could match both the biological rhythm of marine microbes and the short time scale of extreme weather events. Our results show that microbial networks changed from year to year depending on conditions. In addition, individual taxa became less interconnected and changed neighbours, which revealed an unfaithful relationship between marine microorganisms. This unexpected pattern suggests possible switches between organisms that have similar specific functions, or hints at the presence of organisms that share similar environmental niches without interacting. Despite the observed annual changes, the time series showed re-occurring communities that appear to recover from perturbations. Changing co-occurrence patterns between marine microorganisms may allow the long-term stability of ecosystems exposed to contrasting meteorological events.
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Affiliation(s)
- Stefan Lambert
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - François-Yves Bouget
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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19
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Sánchez O, Ferrera I, Mabrito I, Gazulla CR, Sebastián M, Auladell A, Marín-Vindas C, Cardelús C, Sanz-Sáez I, Pernice MC, Marrasé C, Sala MM, Gasol JM. Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton. Sci Rep 2020; 10:19773. [PMID: 33188261 PMCID: PMC7666142 DOI: 10.1038/s41598-020-76590-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022] Open
Abstract
Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.
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Affiliation(s)
- Olga Sánchez
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, 29640, Fuengirola, Málaga, Spain. .,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.
| | - Isabel Mabrito
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain
| | - Carlota R Gazulla
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalunya, Spain.,Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.,Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria (ULPGC), Telde, 35214, Spain
| | - Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Carolina Marín-Vindas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain.,Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, 40101, Costa Rica
| | - Clara Cardelús
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Massimo C Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Cèlia Marrasé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Catalunya, Spain
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20
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Ferrera I, Reñé A, Funosas D, Camp J, Massana R, Gasol JM, Garcés E. Assessment of microbial plankton diversity as an ecological indicator in the NW Mediterranean coast. MARINE POLLUTION BULLETIN 2020; 160:111691. [PMID: 33181960 DOI: 10.1016/j.marpolbul.2020.111691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
High-throughput sequencing of microbial assemblages has been proposed as an alternative methodology to the traditional ones used in marine monitoring and environmental assessment. Here, we evaluated pico- and nanoplankton diversity as ecological indicators in NW Mediterranean coastal waters by comparing their diversity in samples subjected to varying degrees of continental pressures. Using metabarcoding of the 16S and 18S rRNA genes, we explored whether alphadiversity indices, abundance of Operational Taxonomic Units and taxonomic groups (and their ratios) provide information on the ecological quality of coastal waters. Our results revealed that only eukaryotic diversity metrics and a limited number of prokaryotic and eukaryotic taxa displayed potential in assessing continental influences in our surveyed area, resulting thus in a restrained potential of microbial plankton diversity as an ecological indicator. Therefore, incorporating microbial plankton diversity in environmental assessment could not always result in a significant improvement of current marine monitoring strategies.
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Affiliation(s)
- Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain; Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Fuengirola, Málaga, Spain.
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - David Funosas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Jordi Camp
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain.
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21
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Zhang H, Wang Y, Huang T, Liu K, Huang X, Ma B, Li N, Sekar R. Mixed-culture aerobic anoxygenic photosynthetic bacterial consortia reduce nitrate: Core species dynamics, co-interactions and assessment in raw water of reservoirs. BIORESOURCE TECHNOLOGY 2020; 315:123817. [PMID: 32683291 DOI: 10.1016/j.biortech.2020.123817] [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: 06/07/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Three consortia of mixed-culture Aerobic Anoxygenic Photosynthetic Bacteria (AAPB) with excellent aerobic denitrifying ability were isolated from drinking water source reservoirs. The results showed that the removal of dissolved organic carbon (DOC) and nitrate nitrogen (NO3--N) by mixed-culture AAPB were higher than 90% and 99%, respectively. The Illumina MiSeq sequencing of pufM gene revealed that the dominant genera and their relative abundance changed over the culture periods. Sphingomonas sanxanigenens was the most dominant species observed at 9 h, whereas at 48 h, the most abundant species was Rhodobacter blasticus. A network analysis demonstrated that the co-interactions among the different genera were complex and variable. Mixed-culture AAPB removed more than 30% of NO3--N and 25% of DOC from the source water and this study suggests that mixed-culture AAPB can be regarded as a latent denitrifying microbial inoculum in the reservoir raw water treatment.
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Affiliation(s)
- Haihan Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Yan Wang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Kaiwen Liu
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Nan Li
- Shaanxi Key Laboratory of Environmental Engineering, Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Municipal and Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
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22
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Ruiz-González C, Garcia-Chaves MC, Ferrera I, Niño-García JP, Del Giorgio PA. Taxonomic differences shape the responses of freshwater aerobic anoxygenic phototrophic bacterial communities to light and predation. Mol Ecol 2020; 29:1267-1283. [PMID: 32147876 DOI: 10.1111/mec.15404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/29/2022]
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are a phylogenetically diverse and ubiquitous group of prokaryotes that use organic matter but can harvest light using bacteriochlorophyll a. Although the factors regulating AAP ecology have long been investigated through field surveys, the few available experimental studies have considered AAPs as a group, thus disregarding the potential differential responses between taxonomically distinct AAP assemblages. Here, we used sequencing of the pufM gene to describe the diversity of AAPs in 10 environmentally distinct temperate lakes, and to investigate the taxonomic responses of AAP communities in these lakes when subjected to similar experimental manipulations of light and predator removal. The studied communities were clearly dominated by Limnohabitans AAP but presented a clear taxonomic segregation between lakes presumably driven by local conditions, which was maintained after experimental manipulations. Predation reduction (but not light exposure) caused significant compositional shifts across most assemblages, but the magnitude of these changes could not be clearly related to changes in bulk AAP abundances or taxonomic richness of AAP assemblages during experiments. Only a few operational taxonomic units, which differed taxonomically between lakes, were found to respond positively during experimental treatments. Our results highlight that different freshwater AAP communities respond differently to similar control mechanisms, highlighting that in-depth knowledge on AAP diversity is essential to understand the ecology and potential role of these photoheterotrophs.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain.,Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, Málaga, Spain
| | - Juan Pablo Niño-García
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Paul A Del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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