101
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Wang P, Li J, Luo X, Ahmad M, Duan L, Yin L, Fang B, Li S, Yang Y, Jiang L, Li W. Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13949] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Jia‐Ling Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Xiao‐Qing Luo
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Li Duan
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Ling‐Zi Yin
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
| | - Shan‐Hui Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Lin Jiang
- School of Biological Sciences Georgia Institute of Technology Atlanta GA USA
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
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102
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Wang Y, Li Z, Ma L, Li G, Han K, Liu Z, Wang H, Xu B. The Native Dietary Habits of the Two Sympatric Bee Species and Their Effects on Shaping Midgut Microorganisms. Front Microbiol 2021; 12:738226. [PMID: 34690980 PMCID: PMC8529121 DOI: 10.3389/fmicb.2021.738226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 12/27/2022] Open
Abstract
The intestinal microbial community composition of different bee species typically has host specificity, yet little is known about the underlying formation mechanism. There are signs that dietary habits vary in different bee species, suggesting that there may be close relationships between dietary habits and intestinal microorganisms. We explored this hypothesis by comparing the dietary habits and gut microbiota of two common bee species (Apis mellifera L. and Apis cerana cerana) in China. Bee bread and midgut samples from wild and laboratory-reared bees were collected, and the differences in intestinal microbial community composition and growth and development before and after the change in dietary habits of different bee species were compared. We found that the two sympatric species had different dietary specializations and similar metagenomic diversities. The microbiota composition differed between the two species. Moreover, we revealed that changes in native dietary habits destroyed the intestinal microbiota community composition, negatively affecting the growth and development of honeybees.
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Affiliation(s)
- Ying Wang
- Department of Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhenfang Li
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Lanting Ma
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Guilin Li
- College of Life Sciences, Qufu Normal University, Jining, China
| | - Kai Han
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
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103
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Deng Y, Huang H, Lei F, Fu S, Zou K, Zhang S, Liu X, Jiang L, Liu H, Miao B, Liang Y. Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period. Front Microbiol 2021; 12:698703. [PMID: 34671323 PMCID: PMC8521191 DOI: 10.3389/fmicb.2021.698703] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/06/2021] [Indexed: 11/23/2022] Open
Abstract
Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from Ginkgo leaves at five different sampling times. The results indicated that the bacterial community structure varied during leaf developmental stage. Bacterial diversity was observed to be the highest at T2 stage and the lowest at T1 stage. Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes were found as the dominant phyla. The major genera also showed consistency across sampling times, but there was a significant variation in their abundance, such as Bacillus, Lysinibacillus, and Staphylococcus. Significant correlations were observed between endophytic bacteria and flavonoids. Especially, Staphylococcus showed a significant positive correlation with quercetin, and changes in the abundance of Staphylococcus also showed a strong correlation with flavonoid content. In order to determine the effect of flavonoids on endophytic bacteria of Ginkgo leaves, an extracorporeal culture of related strains (a strain of Staphylococcus and a strain of Deinococcus) was performed, and it was found that the effect of flavonoids on them remained consistent. The predicted result of Tax4Fun2 revealed that flavonoids might lead to a lower abundance of endophytic microorganisms, which further proved the correlation between bacterial communities and flavonoids. This study provided the first insight into the bacterial community composition during the development of Ginkgo leaves and the correlation between the endophytic bacteria and flavonoids.
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Affiliation(s)
- Yan Deng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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104
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He D, Zheng J, Ren L, Wu QL. Substrate type and plant phenolics influence epiphytic bacterial assembly during short-term succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148410. [PMID: 34146816 DOI: 10.1016/j.scitotenv.2021.148410] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
In natural ecosystems, large amounts of epiphytic bacteria live on the surfaces of submerged plants or non-biological substrates. Although it contributes greatly to host plant health or ecological functions in waters, little is known about the temporal dynamics and assembly mechanisms of epiphytic bacteria. To test whether host plant chemistry leads to divergent community dynamics, we investigated the fine scale temporal community successions of both epiphytic bacteria and the bacterioplankton of the surrounding water in two submerged plants and one non-biological artificial substance. We first observed differentiated epiphytic or surrounding water bacterial communities for different substrates in small spaces (approximately 1 m × 1 m). Selection played dominant roles in affecting the assembly of epiphytic bacteria in the high-phenolic plant Hydrilla verticillata, while for the artificial substance and the low-phenolic plant Vallisneria natans, drift and dispersal drove the assembly of both epiphytic bacteria and bacterioplankton. The higher selection may also contribute to higher turnover rates in both bacterioplankton and epiphytic communities of H. verticillata, with the latter changing drastically in approximately one week. Epiphytic bacteria in H. verticillata developed more complex networks with a higher proportion of positive links, suggesting that more intense interactions such as mutualism or facilitation may exist within epiphytic bacterial communities of the high-phenolic plant. Our results also implied that for the submerged macrophytes used in biological purification, the dynamics of epiphytic biofilm in the purification-related functional capacities might also be considered.
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Affiliation(s)
- Dan He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jiuwen Zheng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lijuan Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Department of Ecology, Institute of Hydrobiology, Jinan University, Guangzhou 510632, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino Danish Center for Science and Education, University of Chinese Academy of Sciences, Beijing, China.
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105
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Matsumoto K, Sakami T, Watanabe T, Taniuchi Y, Kuwata A, Kakehi S, Engkong T, Igarashi Y, Kinoshita S, Asakawa S, Hattori M, Watabe S, Ishino Y, Kobayashi T, Gojobori T, Ikeo K. Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters. PLoS One 2021; 16:e0257862. [PMID: 34637433 PMCID: PMC8509957 DOI: 10.1371/journal.pone.0257862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/14/2021] [Indexed: 12/05/2022] Open
Abstract
The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.
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Affiliation(s)
- Kaoru Matsumoto
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (KM); (KI)
| | - Tomoko Sakami
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Tsuyoshi Watanabe
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Yukiko Taniuchi
- Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Akira Kuwata
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Shigeho Kakehi
- Tohoku National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Shiogama, Miyagi, Japan
| | - Tan Engkong
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yoji Igarashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takashi Gojobori
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazuho Ikeo
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (KM); (KI)
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106
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Korlević M, Markovski M, Zhao Z, Herndl GJ, Najdek M. Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces. Front Microbiol 2021; 12:671342. [PMID: 34603223 PMCID: PMC8482799 DOI: 10.3389/fmicb.2021.671342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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107
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Cai W, Zhao M, Kong J, Riggio S, Finnigan T, Stuckey D, Guo M. Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater. iScience 2021; 24:102958. [PMID: 34466784 PMCID: PMC8384924 DOI: 10.1016/j.isci.2021.102958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/11/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023] Open
Abstract
We investigated the short-term dynamics of microbial composition and function in bioreactors with inocula collected from full-scale and laboratory-based anaerobic digestion (AD) systems. The Bray-Curtis dissimilarity of both inocula was approximately 10% of the predicted Kyoto Encyclopedia of Genes and Genomes pathway and 40% of the taxonomic composition and yet resulted in a similar performance in methane production, implying that the variation of community composition may be decoupled from performance. However, the significant correlation of volatile fatty acids with taxonomic variation suggested that the pathways of AD could be different because of the varying genus. The predicted function of the significantly varying genus was mostly related to fermentation, which strengthened the conclusion that most microbial variation occurred within the fermentative species and led to alternative routes to result in similar methane production in methanogenic bioreactors. This finding sheds some light on the understanding of AD community regulation, which depends on the aims to recover intermediates or methane.
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Affiliation(s)
- Weiwei Cai
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China.,Department of Engineering, King's College London, London WC2R 2LS, UK
| | - Mingxing Zhao
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, UK.,Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Jianyao Kong
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Silvio Riggio
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Tim Finnigan
- Quorn Foods, Station Road, Stokesley, North Yorkshire TS9 7AB, UK
| | - David Stuckey
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Miao Guo
- Department of Engineering, King's College London, London WC2R 2LS, UK.,Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
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108
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Dong Y, Sanford RA, Connor L, Chee-Sanford J, Wimmer BT, Iranmanesh A, Shi L, Krapac IG, Locke RA, Shao H. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. WATER RESEARCH 2021; 202:117431. [PMID: 34320445 DOI: 10.1016/j.watres.2021.117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
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Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, USA
| | | | | | | | | | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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109
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Lara EG, van der Windt I, Molenaar D, de Vos MGJ, Melkonian C. Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. Genes (Basel) 2021; 12:genes12081221. [PMID: 34440394 PMCID: PMC8393552 DOI: 10.3390/genes12081221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 02/01/2023] Open
Abstract
The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.
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Affiliation(s)
- Elena G. Lara
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | | | - Douwe Molenaar
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
| | - Marjon G. J. de Vos
- GELIFES, Universtity of Groningen, 9747 AG Groningen, The Netherlands;
- Correspondence: (M.G.J.d.V.); (C.M.)
| | - Chrats Melkonian
- Systems Biology Lab, AIMMS, Vrije Universiteit, 1081 HZ Amsterdam, The Netherlands; (E.G.L.); (D.M.)
- Correspondence: (M.G.J.d.V.); (C.M.)
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110
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Wang C, Liu S, Wang P, Chen J, Wang X, Yuan Q, Ma J. How sediment bacterial community shifts along the urban river located in mining city. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42300-42312. [PMID: 33811632 DOI: 10.1007/s11356-020-12031-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Bacterial communities play critical roles in biogeochemical cycles and serve as sensitive indicators of environmental fluctuation. However, the influence of mineral resource exploitation on shaping the bacterial communities in the urban river is still ambiguous. In this study, high-throughput sequencing was used to determine the spatial distribution of the sediment bacterial communities along an urban river in the famous mining city Panzhihua of China. The results showed that mineral resource exploitation had a significant impact on the urban river bacterial community structure but not on the bacterial ecological functions. Distinct families of bacteria often associated with nutrients (i.e., Comamonadaceae and Sphingomonadaceae) and metal contaminants (i.e., Rhodobacteraceae) were more predominant in the residential and mining area, respectively. Relative to dispersal dynamics, environmentally induced species sorting may primarily influence bacterial community structure. Heavy metals and sediment physicochemical properties had both similar and significant influence on shaping bacterial community structure. Among heavy metals, essential metal elements explained more rates of bacterial variation than toxic metals at moderate contaminant levels. Moreover, the bacteria with multiple metal resistances identified in culture-dependent experiments were probably not suitable for indicating heavy metal contamination in field research. Thus, several sensitive bacterial genera such as Rhodobacter, Hylemonella, and Dechloromonas were identified as potential bioindicators to monitor metals (iron and titanium) and nutrients (phosphorus and organic carbon) in the river ecosystem of the Panzhihua region. Together, these results profiled the coupling effect of urbanization and mineral resource utilization on shaping sediment bacterial communities in urban rivers.
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Affiliation(s)
- Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Sheng Liu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China.
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
| | - Jingjie Ma
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, No.1 Xikang Road, Nanjing, 210098, China
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111
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Aleksova M, Kenarova A, Boteva S, Georgieva S, Chanev C, Radeva G. Effects of increasing concentrations of fungicide Quadris R on bacterial functional profiling in loamy sand soil. Arch Microbiol 2021; 203:4385-4396. [PMID: 34117918 DOI: 10.1007/s00203-021-02423-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 11/29/2022]
Abstract
A mesocosm experiment was conducted to assess the side effects of the fungicide QuadrisR on soil bacterial functioning. QuadrisR was applied to a loamy sand soil at increasing concentrations (0.0-35.0 mg kg-1 dry soil) calculated according to its active ingredient azoxystrobin (Az). Soil sampling was carried out from the 1st to the 120th day of soil incubation to determine the changes occurred in bacterial catabolism using the technique of community-level physiological profiling (CLPP) via Biolog EcoPlates™. It was found that the field recommended fungicide concentration (2.90 mg kg-1 dry soil) altered mostly the low-available Biolog carbon sources (< 0.50 optical density (OD)), whereas the fungicide higher concentrations (14.65 and 35.00 mg kg-1 dry soil) were effective also on medium (0.50-1.00 OD) and highly (> 1.00 OD) utilizable ones. Pearson correlation analysis revealed that the main environmental factors correlated with the utilization rates of Biolog carbon sources (CSs) were soil nutrients and pH. No linear relationships were found between Az soil residues and the use of CSs. We concluded that QuadrisR affects bacterial catabolic profiles in loamy sand soils through soil acidification and altering soil nutrient pool. The study also revealed that CLPP and EcoPlate™ are useful practical tools for testing the fungicide ecotoxicity.
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Affiliation(s)
- Michaella Aleksova
- Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
| | - Anelia Kenarova
- Department of Ecology and Nature Conservation, Faculty of Biology, Sofia University "St. Kl. Ohridski", 8 Dragan Tsankov Blvd, 1164, Sofia, Bulgaria
| | - Silvena Boteva
- Department of Ecology and Nature Conservation, Faculty of Biology, Sofia University "St. Kl. Ohridski", 8 Dragan Tsankov Blvd, 1164, Sofia, Bulgaria.
| | - Stela Georgieva
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1 James Bourchier Blvd, 1164, Sofia, Bulgaria
| | - Christo Chanev
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kl. Ohridski", 1 James Bourchier Blvd, 1164, Sofia, Bulgaria
| | - Galina Radeva
- Institute of Molecular Biology "Acad. Roumen Tsanev", Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 21, 1113, Sofia, Bulgaria
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112
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Korlević M, Markovski M, Zhao Z, Herndl GJ, Najdek M. Selective DNA and Protein Isolation From Marine Macrophyte Surfaces. Front Microbiol 2021; 12:665999. [PMID: 34108951 PMCID: PMC8180852 DOI: 10.3389/fmicb.2021.665999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/30/2021] [Indexed: 12/04/2022] Open
Abstract
Studies of unculturable microbes often combine methods, such as 16S rRNA sequencing, metagenomics, and metaproteomics. To apply these techniques to the microbial community inhabiting the surfaces of marine macrophytes, it is advisable to perform a selective DNA and protein isolation prior to the analysis to avoid biases due to the host material being present in high quantities. Two protocols for DNA and protein isolation were adapted for selective extractions of DNA and proteins from epiphytic communities inhabiting the surfaces of two marine macrophytes, the seagrass Cymodocea nodosa and the macroalga Caulerpa cylindracea. Protocols showed an almost complete removal of the epiphytic community regardless of the sampling season, station, settlement, or host species. The obtained DNA was suitable for metagenomic and 16S rRNA sequencing, while isolated proteins could be identified by mass spectrometry. Low presence of host DNA and proteins in the samples indicated a high specificity of the protocols. The procedures are based on universally available laboratory chemicals making the protocols widely applicable. Taken together, the adapted protocols ensure an almost complete removal of the macrophyte epiphytic community. The procedures are selective for microbes inhabiting macrophyte surfaces and provide DNA and proteins applicable in 16S rRNA sequencing, metagenomics, and metaproteomics.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands.,Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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113
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Lei F, Liu X, Huang H, Fu S, Zou K, Zhang S, Zhou L, Zeng J, Liu H, Jiang L, Miao B, Liang Y. The Macleaya cordata Symbiont: Revealing the Effects of Plant Niches and Alkaloids on the Bacterial Community. Front Microbiol 2021; 12:681210. [PMID: 34177865 PMCID: PMC8219869 DOI: 10.3389/fmicb.2021.681210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Endophytes are highly associated with plant growth and health. Exploring the variation of bacterial communities in different plant niches is essential for understanding microbe-plant interactions. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from the rhizospheric soil and different parts of the Macleaya cordata. The results indicated that the bacterial community structure varied widely among compartments. Bacterial diversity was observed to be the highest in the rhizospheric soil and the lowest in fruits. Proteobacteria, Actinobacteria, and Bacteroidetes were found as the dominant phyla. The genera Sphingomonas (∼47.77%) and Methylobacterium (∼45.25%) dominated in fruits and leaves, respectively. High-performance liquid chromatography (HPLC) was employed to measure the alkaloid content of different plant parts. Significant correlations were observed between endophytic bacteria and alkaloids. Especially, Sphingomonas showed a significant positive correlation with sanguinarine and chelerythrine. All four alkaloids were negatively correlated with the microbiota of stems. The predicted result of PICRUST2 revealed that the synthesis of plant alkaloids might lead to a higher abundance of endophytic microorganisms with genes related to alkaloid synthesis, further demonstrated the correlation between bacterial communities and alkaloids. This study provided the first insight into the bacterial community composition in different parts of Macleaya cordata and the correlation between the endophytic bacteria and alkaloids.
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Affiliation(s)
- Fangying Lei
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Haonan Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shaodong Fu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Kai Zou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Li Zhou
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Luhua Jiang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
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114
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Chan J, Geng D, Pan B, Zhang Q, Xu Q. Metagenomic Insights Into the Structure and Function of Intestinal Microbiota of the Hadal Amphipods. Front Microbiol 2021; 12:668989. [PMID: 34163447 PMCID: PMC8216301 DOI: 10.3389/fmicb.2021.668989] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Hadal trenches are the deepest known areas of the ocean. Amphipods are considered to be the dominant scavengers in the hadal food webs. The studies on the structure and function of the hadal intestinal microbiotas are largely lacking. Here, the intestinal microbiotas of three hadal amphipods, Hirondellea gigas, Scopelocheirus schellenbergi, and Alicella gigantea, from Mariana Trench, Marceau Trench, and New Britain Trench, respectively, were investigated. The taxonomic analysis identified 358 microbial genera commonly shared within the three amphipods. Different amphipod species possessed their own characteristic dominant microbial component, Psychromonas in H. gigas and Candidatus Hepatoplasma in A. gigantea and S. schellenbergi. Functional composition analysis showed that “Carbohydrate Metabolism,” “Lipid Metabolism,” “Cell Motility,” “Replication and Repair,” and “Membrane Transport” were among the most represented Gene Ontology (GO) Categories in the gut microbiotas. To test the possible functions of “Bacterial Chemotaxis” within the “Cell Motility” category, the methyl-accepting chemotaxis protein (MCP) gene involved in the “Bacterial Chemotaxis” pathway was obtained and used for swarming motility assays. Results showed that bacteria transformed with the gut bacterial MCP gene showed significantly faster growths compared with the control group, suggesting MCP promoted the bacterial swimming capability and nutrient utilization ability. This result suggested that hadal gut microbes could promote their survival in poor nutrient conditions by enhancing chemotaxis and motility. In addition, large quantities of probiotic genera were detected in the hadal amphipod gut microbiotas, which indicated that those probiotics would be possible contributors for promoting the host’s growth and development, which could facilitate adaptation of hadal amphipods to the extreme environment.
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Affiliation(s)
- Jiulin Chan
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Daoqiang Geng
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Binbin Pan
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qiming Zhang
- Shanghai Rainbowfish Ocean Technology Co., Ltd, Shanghai, China
| | - Qianghua Xu
- Key Laboratory of Sustainable Exploitation of Oceanic Fisheries Resources, Ministry of Education, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.,Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.,National Distant-water Fisheries Engineering Research Center, Shanghai Ocean University, Shanghai, China
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115
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Composition and Associations of the Infant Gut Fungal Microbiota with Environmental Factors and Childhood Allergic Outcomes. mBio 2021; 12:e0339620. [PMID: 34060330 PMCID: PMC8263004 DOI: 10.1128/mbio.03396-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although often neglected in gut microbiota studies, recent evidence suggests that imbalanced, or dysbiotic, gut mycobiota (fungal microbiota) communities in infancy coassociate with states of bacterial dysbiosis linked to inflammatory diseases such as asthma. In the present study, we (i) characterized the infant gut mycobiota at 3 months and 1 year of age in 343 infants from the CHILD Cohort Study, (ii) defined associations among gut mycobiota community composition and environmental factors for the development of inhalant allergic sensitization (atopy) at age 5 years, and (iii) built a predictive model for inhalant atopy status at age 5 years using these data. We show that in Canadian infants, fungal communities shift dramatically in composition over the first year of life. Early-life environmental factors known to affect gut bacterial communities were also associated with differences in gut fungal community alpha diversity, beta diversity, and/or the relative abundance of specific fungal taxa. Moreover, these metrics differed among healthy infants and those who developed inhalant allergic sensitization (atopy) by age 5 years. Using a rationally selected set of early-life environmental factors in combination with fungal community composition at 1 year of age, we developed a machine learning logistic regression model that predicted inhalant atopy status at 5 years of age with 81% accuracy. Together, these data suggest an important role for the infant gut mycobiota in early-life immune development and indicate that early-life behavioral or therapeutic interventions have the potential to modify infant gut fungal communities, with implications for an infant's long-term health. IMPORTANCE Recent evidence suggests an immunomodulatory role for commensal fungi (mycobiota) in the gut, yet little is known about the composition and dynamics of early-life gut fungal communities. In this work, we show for the first time that the composition of the gut mycobiota of Canadian infants changes dramatically over the course of the first year of life, is associated with environmental factors such as geographical location, diet, and season of birth, and can be used in conjunction with knowledge of a small number of key early-life factors to predict inhalant atopy status at age 5 years. Our study highlights the importance of considering fungal communities as indicators or inciters of immune dysfunction preceding the onset of allergic disease and can serve as a benchmark for future studies aiming to examine infant gut fungal communities across birth cohorts.
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116
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Yang Y. Emerging Patterns of Microbial Functional Traits. Trends Microbiol 2021; 29:874-882. [PMID: 34030967 DOI: 10.1016/j.tim.2021.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 01/03/2023]
Abstract
Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.
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Affiliation(s)
- Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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117
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Fadiji AE, Kanu JO, Babalola OO. Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach. Arch Microbiol 2021; 203:3605-3613. [PMID: 33973044 DOI: 10.1007/s00203-021-02354-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 01/03/2023]
Abstract
Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Jerry Onyemaechi Kanu
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag X2046, Mmabatho, South Africa.
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118
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Doering T, Wall M, Putchim L, Rattanawongwan T, Schroeder R, Hentschel U, Roik A. Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues. MICROBIOME 2021; 9:102. [PMID: 33957989 PMCID: PMC8103578 DOI: 10.1186/s40168-021-01053-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/18/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding. RESULTS Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context. CONCLUSIONS Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.
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Affiliation(s)
- Talisa Doering
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Marlene Wall
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Lalita Putchim
- Phuket Marine Biological Center (PMBC), Phuket, Thailand
| | | | | | - Ute Hentschel
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Anna Roik
- GEOMAR, Helmholtz Centre for Ocean Research, Kiel, Germany.
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119
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Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, Dittami SM. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 2021; 9:e11344. [PMID: 33996285 PMCID: PMC8106915 DOI: 10.7717/peerj.11344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/03/2021] [Indexed: 01/29/2023] Open
Abstract
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
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Affiliation(s)
- Elham Karimi
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Enora Geslain
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France.,FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Arnaud Belcour
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Méziane Aïte
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Anne Siegel
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Erwan Corre
- FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Simon M Dittami
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
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120
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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121
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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122
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Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments. Appl Microbiol Biotechnol 2021; 105:3843-3857. [PMID: 33914137 DOI: 10.1007/s00253-021-11283-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/20/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Wheat is the core food crop in bioregenerative life support systems (BLSSs). In confined isolation environments, wheat growth suffers from a lack of stable microbial communities and is susceptible to pathogenic infections due to the culture substrate's limitations. To overcome this limitation, the time series changes of wheat rhizosphere microorganisms in wheat production must be understood. In the present study, we examined the rhizosphere microbial samples from wheat at four different growth stages from plants collected from a BLSS plant cabin. We employed bioinformatics analysis strategies to analyze the characteristics of species composition, function prediction, and community network. The species composition of wheat rhizosphere microorganisms was relatively stable in the seedling, tillering, and flowering stages in confined isolation environments. However, we observed marked microbial changes at mature stages. The results of functional prediction analysis suggest that the rhizosphere microbial community function of "Energy metabolism" gradually decreased, and the function of "Transmembrane transport" gradually increased during wheat development. The construction of the rhizosphere microbial community is non-random, scale-free and has the characteristics of a small world. We found the tillering stage to be more complex than the other stages. Our study reveals the composition characteristics, functional changes, and community structure fluctuations of rhizosphere bacteria at different development stages of wheat in the isolated and controlled environment, providing a theoretical basis for the efficient production of BLSS plant systems. KEY POINTS: • We collected wheat rhizosphere microorganisms at different stages in a confined isolation environment. • The diversity, composition, function, and network structure of rhizosphere bacteria were analyzed. • The effect of different wheat stages on the composition, function, and network structure of rhizosphere microorganisms was speculated.
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123
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Smith DJ, Tan JY, Powers MA, Lin XN, Davis TW, Dick GJ. Individual Microcystis colonies harbour distinct bacterial communities that differ by Microcystis oligotype and with time. Environ Microbiol 2021; 23:3020-3036. [PMID: 33830633 DOI: 10.1111/1462-2920.15514] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 03/11/2021] [Accepted: 04/06/2021] [Indexed: 12/31/2022]
Abstract
Interactions between bacteria and phytoplankton in the phycosphere have impacts at the scale of whole ecosystems, including the development of harmful algal blooms. The cyanobacterium Microcystis causes toxic blooms that threaten freshwater ecosystems and human health globally. Microcystis grows in colonies that harbour dense assemblages of other bacteria, yet the taxonomic composition of these phycosphere communities and the nature of their interactions with Microcystis are not well characterized. To identify the taxa and compositional variance within Microcystis phycosphere communities, we performed 16S rRNA V4 region amplicon sequencing on individual Microcystis colonies collected biweekly via high-throughput droplet encapsulation during a western Lake Erie cyanobacterial bloom. The Microcystis phycosphere communities were distinct from microbial communities in whole water and bulk phytoplankton seston in western Lake Erie but lacked 'core' taxa found across all colonies. However, dissimilarity in phycosphere community composition correlated with sampling date and the Microcystis 16S rRNA oligotype. Several taxa in the phycosphere were specific to and conserved with Microcystis of a single oligotype or sampling date. Together, this suggests that physiological differences between Microcystis strains, temporal changes in strain phenotypes, and the composition of seeding communities may impact community composition of the Microcystis phycosphere.
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Affiliation(s)
- Derek J Smith
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - James Y Tan
- Department of Chemical Engineering, The University of Michigan, NCRC, 2800 Plymouth Rd., Ann Abor, MI, 48109, USA
| | - McKenzie A Powers
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Xiaoxia N Lin
- Department of Chemical Engineering, The University of Michigan, NCRC, 2800 Plymouth Rd., Ann Abor, MI, 48109, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Life Sciences Building, Corner of N. College Dr and E. Merry Avenue, Bowling Green, OH, 43403, USA
| | - Gregory J Dick
- Department of Earth & Environmental Science, The University of Michigan, 1100 N. University Building, 1100 N. University Avenue, Ann Arbor, MI, 48109, USA
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Environmental factors shape the epiphytic bacterial communities of Gracilariopsis lemaneiformis. Sci Rep 2021; 11:8671. [PMID: 33883606 PMCID: PMC8060329 DOI: 10.1038/s41598-021-87977-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
Macroalgae host various symbionts on their surface, which play a critical role in their growth and development processes. However, there is still incomplete understanding of this epiphytic bacteria-host algae interactions. This study comprehensively analysed variation of the epiphytic bacterial communities (EBC) composition of red macroalga Gracilariopsis lemaneiformis at different geographic locations and environmental factors (i.e., nitrogen and phosphorus), which shape the EBC composition of G. lemaneiformis. The composition and structure of EBC were characterized using high throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that epiphytic bacteria varied significantly among three different geographic locations in China, i.e., Nan'ao Island (NA), Lianjiang County (LJ), and Nanri Island (NR). Redundancy analysis (RDA) showed that the relative abundance of Bacteroidetes, Firmicutes, Verrucomicrobia, and Epsilonbacteraeota at NR were strongly positively correlated with total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3-N), and dissolved inorganic nitrogen (DIN), but negatively correlated with nitrite nitrogen (NO2-N). The relative abundance of Cyanobacteria at NA and LJ were strongly positively correlated with NO2-N, but negatively correlated with TN, TP, NO3-N, and DIN. Besides, the Mantel test results indicated that the EBC composition was significantly correlated with these environmental factors, which was also confirmed by Spearman correlation analysis. Thus, environmental factors such as NO3-N and DIN play a key role in the community composition of epiphytic bacteria on G. lemaneiformis. This study provides important baseline knowledge on the community composition of epiphytic bacteria on G. lemaneiformis and shows correlation between different epiphytic bacteria and their surrounding environmental factors.
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125
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Yu J, Tang SN, Lee PKH. Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5312-5323. [PMID: 33784458 DOI: 10.1021/acs.est.0c06732] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.
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Affiliation(s)
- Jinjin Yu
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Siang Nee Tang
- Facility Management and Environmental Engineering, TAL Group, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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126
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Hudon SF, Zaiats A, Roser A, Roopsind A, Barber C, Robb BC, Pendleton BA, Camp MJ, Clark PE, Davidson MM, Frankel‐Bricker J, Fremgen‐Tarantino M, Forbey JS, Hayden EJ, Richards LA, Rodriguez OK, Caughlin TT. Unifying community detection across scales from genomes to landscapes. OIKOS 2021. [DOI: 10.1111/oik.08393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Anna Roser
- Boise State Univ. Boise ID USA
- Center for Natural Climate Solutions, Conservation International Arlington VA USA
| | | | | | | | | | | | - Patrick E. Clark
- Northwest Watershed Research Center, USDA Agricultural Research Service Boise ID USA
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127
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Estrela S, Sánchez Á, Rebolleda-Gómez M. Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology. Front Microbiol 2021; 12:657467. [PMID: 33897672 PMCID: PMC8062719 DOI: 10.3389/fmicb.2021.657467] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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128
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Nousias O, Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics 2021; 59:100866. [PMID: 33812777 DOI: 10.1016/j.margen.2021.100866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Microbial communities play fundamental roles in association with marine algae; in fact, they are recognized to be actively involved in growth and morphogenesis of the algae. Porphyra purpurea is a red alga commonly found in the intertidal zone with a high economic value, however little is known about the bacterial species associated with this genus. Here we report the bacterial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets. These were analyzed with Methaplan3 to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared these results to the 16S rRNA metagenomic analysis pipeline of the MGnify database to evaluate both methods. Kraken2 was used to verify and support the results, as a complementary classification method to Metaphlan3. This approach highlighted the different taxonomic resolution of a 16S rRNA OTU-based method compared to the pan-genome approach deployed by Metaphlan3 and complemented by Kraken2. The results presented here provide valuable preliminary data on the putative host-associated bacterial species of P. purpurea.
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Affiliation(s)
- Orestis Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece; Department of Biology, University of Crete, Greece.
| | - Federica Montesanto
- Department of Biology, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy; CoNISMa, Piazzale Flaminio 9, 00197 Roma, Italy.
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129
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Pascual-García A. Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework : Comment to ``A conceptual framework for the phylogenetically-constrained assembly of microbial communities''. MICROBIOME 2021; 9:73. [PMID: 33766138 PMCID: PMC7993459 DOI: 10.1186/s40168-021-01023-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
In this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology. Video Abstract.
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130
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Goodrich-Blair H. Interactions of host-associated multispecies bacterial communities. Periodontol 2000 2021; 86:14-31. [PMID: 33690897 DOI: 10.1111/prd.12360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.
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Affiliation(s)
- Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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131
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Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. THE ISME JOURNAL 2021; 15:807-817. [PMID: 33558686 PMCID: PMC8027169 DOI: 10.1038/s41396-020-00815-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/30/2023]
Abstract
Horizontal gene transfer (HGT) is thought to be an important driving force for microbial evolution and niche adaptation and has been show in vitro to occur frequently in biofilm communities. However, the extent to which HGT takes place and what functions are being transferred in more complex and natural biofilm systems remains largely unknown. To address this issue, we investigated here HGT and enrichment of gene functions in the biofilm community of the common kelp (macroalgae) Ecklonia radiata in comparison to microbial communities in the surrounding seawater. We found that HGTs in the macroalgal biofilms were dominated by transfers between bacterial members of the same class or order and frequently involved genes for nutrient transport, sugar and phlorotannin degradation as well as stress responses, all functions that would be considered beneficial for bacteria living in this particular niche. HGT did not appear to be driven by mobile gene elements, indicating rather an involvement of unspecific DNA uptake (e.g. natural transformation). There was also a low overlap between the gene functions subject to HGT and those enriched in the biofilm community in comparison to planktonic community members. This indicates that much of the functionality required for bacteria to live in an E. radiata biofilm might be derived from vertical or environmental transmissions of symbionts. This study enhances our understanding of the relative role of evolutionary and ecological processes in driving community assembly and genomic diversity of biofilm communities.
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132
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Mugge RL, Salerno JL, Hamdan LJ. Microbial Functional Responses in Marine Biofilms Exposed to Deepwater Horizon Spill Contaminants. Front Microbiol 2021; 12:636054. [PMID: 33717029 PMCID: PMC7947620 DOI: 10.3389/fmicb.2021.636054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Marine biofilms are essential biological components that transform built structures into artificial reefs. Anthropogenic contaminants released into the marine environment, such as crude oil and chemical dispersant from an oil spill, may disrupt the diversity and function of these foundational biofilms. To investigate the response of marine biofilm microbiomes from distinct environments to contaminants and to address microbial functional response, biofilm metagenomes were analyzed from two short-term microcosms, one using surface seawater (SSW) and the other using deep seawater (DSW). Following exposure to crude oil, chemical dispersant, and dispersed oil, taxonomically distinct communities were observed between microcosms from different source water challenged with the same contaminants and higher Shannon diversity was observed in SSW metagenomes. Marinobacter, Colwellia, Marinomonas, and Pseudoalteromonas phylotypes contributed to driving community differences between SSW and DSW. SSW metagenomes were dominated by Rhodobacteraceae, known biofilm-formers, and DSW metagenomes had the highest abundance of Marinobacter, associated with hydrocarbon degradation and biofilm formation. Association of source water metadata with treatment groups revealed that control biofilms (no contaminant) harbor the highest percentage of significant KEGG orthologs (KOs). While 70% functional similarity was observed among all metagenomes from both experiments, functional differences between SSW and DSW metagenomes were driven primarily by membrane transport KOs, while functional similarities were attributed to translation and signaling and cellular process KOs. Oil and dispersant metagenomes were 90% similar to each other in their respective experiments, which provides evidence of functional redundancy in these microbiomes. When interrogating microbial functional redundancy, it is crucial to consider how composition and function evolve in tandem when assessing functional responses to changing environmental conditions within marine biofilms. This study may have implications for future oil spill mitigation strategies at the surface and at depth and also provides information about the microbiome functional responses of biofilms on steel structures in the marine built environment.
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Affiliation(s)
- Rachel L Mugge
- Division of Coastal Sciences, School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS, United States
| | - Jennifer L Salerno
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, United States
| | - Leila J Hamdan
- Division of Coastal Sciences, School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, MS, United States
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133
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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134
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The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator. WATER 2021. [DOI: 10.3390/w13040406] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes and seagrass establish symbiotic relationships constituting a functional unit called the holobiont that reacts as a whole to environmental changes. Recent studies have shown that the seagrass microbial associated community varies according to host species, environmental conditions and the host’s health status, suggesting that the microbial communities respond rapidly to environmental disturbances and changes. These changes, dynamics of which are still far from being clear, could represent a sensitive monitoring tool and ecological indicator to detect early stages of seagrass stress. In this review, the state of art on seagrass holobiont is discussed in this perspective, with the aim of disentangling the influence of different factors in shaping it. As an example, we expand on the widely studied Halophila stipulacea’s associated microbial community, highlighting the changing and the constant components of the associated microbes, in different environmental conditions. These studies represent a pivotal contribution to understanding the holobiont’s dynamics and variability pattern, and to the potential development of ecological/ecotoxicological indices. The influences of the host’s physiological and environmental status in changing the seagrass holobiont, alongside the bioinformatic tools for data analysis, are key topics that need to be deepened, in order to use the seagrass-microbial interactions as a source of ecological information.
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135
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Gaube P, Junker RR, Keller A. Changes amid constancy: Flower and leaf microbiomes along land use gradients and between bioregions. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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136
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Clarke LJ, Suter L, King R, Bissett A, Bestley S, Deagle BE. Bacterial epibiont communities of panmictic Antarctic krill are spatially structured. Mol Ecol 2021; 30:1042-1052. [PMID: 33300251 DOI: 10.1111/mec.15771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 12/28/2022]
Abstract
Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven mainly by distance rather than environmental factors, especially for strongly krill-associated bacteria. Estimating the ecological processes driving bacterial community turnover indicated this was driven by bacterial dispersal limitation increasing with geographic distance. Furthermore, divergent epibiont communities generated from a single krill swarm split between aquarium tanks under near-identical conditions suggests physical isolation in itself can cause krill-associated bacterial communities to diverge. Our findings show that Antarctic krill-associated bacterial communities are geographically structured, in direct contrast with the lack of structure observed for krill genetic and genomic data.
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Affiliation(s)
- Laurence J Clarke
- Australian Antarctic Division, Kingston, Tas, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas, Australia.,Antarctic Climate & Ecosystems Cooperative Research Centre, University of Tasmania, Hobart, Tas, Australia
| | - Léonie Suter
- Australian Antarctic Division, Kingston, Tas, Australia
| | - Rob King
- Australian Antarctic Division, Kingston, Tas, Australia
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, Tas, Australia
| | - Sophie Bestley
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, Kingston, Tas, Australia.,Commonwealth Scientific and Industrial Research Organisation, Hobart, Tas, Australia
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137
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Comba González NB, Niño Corredor AN, López Kleine L, Montoya Castaño D. Temporal Changes of the Epiphytic Bacteria Community From the Marine Macroalga Ulva lactuca (Santa Marta, Colombian-Caribbean). Curr Microbiol 2021; 78:534-543. [PMID: 33388936 DOI: 10.1007/s00284-020-02302-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/20/2020] [Indexed: 11/28/2022]
Abstract
Microbial communities live on macroalgal surfaces. The identity and abundance of the bacteria making these epiphytic communities depend on the macroalgal host and the environmental conditions. Macroalgae rely on epiphytic bacteria for basic functions (spore settlement, morphogenesis, growth, and protection against pathogens). However, these marine bacterial-macroalgal associations are still poorly understood for macroalgae inhabiting the Colombian Caribbean. This study aimed at characterizing the epiphytic bacterial community from macroalgae of the species Ulva lactuca growing in La Punta de la Loma (Santa Marta, Colombia). We conducted a 16S rRNA gene sequencing-based study of these microbial communities sampled twice a year between 2014 and 2016. Within these communities, the Proteobacteria, Bacterioidetes, Cyanobacteria, Deinococcus-Thermus and Actinobacteria were the most abundant phyla. At low taxonomic levels, we found high variability among epiphytic bacteria from U. lactuca and bacterial communities associated with macroalgae from Germany and Australia. We observed differences in the bacterial community composition across years driven by abundance shifts of Rhodobacteraceae Hyphomonadaceae, and Flavobacteriaceae, probably caused by an increase of seawater temperature. Our results support the need for functional studies of the microbiota associated with U. lactuca, a common macroalga in the Colombian Caribbean Sea.
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Affiliation(s)
| | - Albert Nicolás Niño Corredor
- Bioprocesses and Bioprospecting Group, Instituto de Biotecnología, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Dolly Montoya Castaño
- Bioprocesses and Bioprospecting Group, Instituto de Biotecnología, Universidad Nacional de Colombia, 14490, Bogotá, AA, Colombia.
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138
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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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139
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Parsons C, Stüeken EE, Rosen CJ, Mateos K, Anderson RE. Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. GEOBIOLOGY 2021; 19:18-34. [PMID: 33108025 PMCID: PMC7894544 DOI: 10.1111/gbi.12419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 05/03/2023]
Abstract
Nitrogen is an essential element to life and exerts a strong control on global biological productivity. The rise and spread of nitrogen-utilizing microbial metabolisms profoundly shaped the biosphere on the early Earth. Here, we reconciled gene and species trees to identify birth and horizontal gene transfer events for key nitrogen-cycling genes, dated with a time-calibrated tree of life, in order to examine the timing of the proliferation of these metabolisms across the tree of life. Our results provide new insights into the evolution of the early nitrogen cycle that expand on geochemical reconstructions. We observed widespread horizontal gene transfer of molybdenum-based nitrogenase back to the Archean, minor horizontal transfer of genes for nitrate reduction in the Archean, and an increase in the proliferation of genes metabolizing nitrite around the time of the Mesoproterozoic (~1.5 Ga). The latter coincides with recent geochemical evidence for a mid-Proterozoic rise in oxygen levels. Geochemical evidence of biological nitrate utilization in the Archean and early Proterozoic may reflect at least some contribution of dissimilatory nitrate reduction to ammonium (DNRA) rather than pure denitrification to N2 . Our results thus help unravel the relative dominance of two metabolic pathways that are not distinguishable with current geochemical tools. Overall, our findings thus provide novel constraints for understanding the evolution of the nitrogen cycle over time and provide insights into the bioavailability of various nitrogen sources in the early Earth with possible implications for the emergence of eukaryotic life.
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Affiliation(s)
- Chris Parsons
- Carleton CollegeNorthfieldMNUSA
- Massachusetts Institute of TechnologyCambridgeMAUSA
| | | | | | | | - Rika E. Anderson
- Carleton CollegeNorthfieldMNUSA
- NASA NExSS Virtual Planetary LaboratoryUniversity of WashingtonSeattleWAUSA
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140
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Li Y, Gao L, Niu L, Zhang W, Yang N, Du J, Gao Y, Li J. Developing a statistical-weighted index of biotic integrity for large-river ecological evaluations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 277:111382. [PMID: 33069143 DOI: 10.1016/j.jenvman.2020.111382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/14/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
The efficiency, accuracy and universality of ecological assessment methods comprise an important foundation for comprehensive assessment and restoration of large river ecological health at the watershed scale. New evaluation metrics and methods are urgently needed to be developed to adapt the characteristics of large rivers, including geographical differences in surface runoff, regional ecological complexity, and seasonal changes. In this study, a bacteria-weighted index of biotic integrity was developed to assess the ecological health of large rivers (lrBW-IBI) based on compositional and functional characteristics of sediment bacterial communities from 33 sections of the lower mainstream of Yangtze River. Five key metrics were determined by range, responsiveness, and redundancy tests. Principal component analysis (PCA), entropy method, criteria importance through intercriteria correlation and random forest were applied to calculate weighted coefficients of key metrics. The optimal lrBW-IBI was observed through the sum of PCA weighted-metrics: the relative abundance of Latescibacteria (0.234), Gemmatimonadaceae (0.149), Nitrospira spp. (0.234), Rhizobiales (0.228), and nitrogenase NifH (0.156). According to PCA based lrBW-IBI, 12.12%, 24.24%, 39.39%, and 24.24% of river sections were labeled excellent, good, moderate, and relatively poor, respectively. The ecological status of the lower mainstream of the Yangtze River did not change significantly across seasons but declined gradually from upstream to downstream. This study provides a new assessment tool for the ecological health of large rivers and highlights the importance of microbial ecological index in river ecology.
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Affiliation(s)
- Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lin Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Jiming Du
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Jie Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
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141
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D’Souza AW, Moodley-Govender E, Berla B, Kelkar T, Wang B, Sun X, Daniels B, Coutsoudis A, Trehan I, Dantas G. Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants. Clin Infect Dis 2020; 71:2858-2868. [PMID: 31832638 PMCID: PMC7778358 DOI: 10.1093/cid/ciz1186] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Prophylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)-exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined. METHODS We analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants. RESULTS Metagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2-1.2] and 6-month mean, 0.85 [95% CI, .1-1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, -0.11 [95% CI, -.15 to -.077]), functional taxonomic (mean, -0.050 [95% CI, -.084 to -.017]), and resistance gene (mean, -0.13 [95% CI, -.17 to -.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure. CONCLUSIONS Cotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.
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Affiliation(s)
- Alaric W D’Souza
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Eshia Moodley-Govender
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Bertram Berla
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Tejas Kelkar
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Bin Wang
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Xiaoqing Sun
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Brodie Daniels
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
- HIV Preventin Research Unit, South African Medical Research Council, Durban, South Africa
| | - Anna Coutsoudis
- Department of Paediatrics and Child Health, University of KwaZulu-Natal, Durban, South Africa
| | - Indi Trehan
- HIV Preventin Research Unit, South African Medical Research Council, Durban, South Africa
- Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, Missouri, USA
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142
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Morphological complexity affects the diversity of marine microbiomes. ISME JOURNAL 2020; 15:1372-1386. [PMID: 33349654 DOI: 10.1038/s41396-020-00856-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Large eukaryotes support diverse communities of microbes on their surface-epibiota-that profoundly influence their biology. Alternate factors known to structure complex patterns of microbial diversity-host evolutionary history and ecology, environmental conditions and stochasticity-do not act independently and it is challenging to disentangle their relative effects. Here, we surveyed the epibiota from 38 sympatric seaweed species that span diverse clades and have convergent morphology, which strongly influences seaweed ecology. Host identity explains most of the variation in epibiont communities and deeper host phylogenetic relationships (e.g., genus level) explain a small but significant portion of epibiont community variation. Strikingly, epibiota community composition is significantly influenced by host morphology and epibiota richness increases with morphological complexity of the seaweed host. This effect is robust after controlling for phylogenetic non-independence and is strongest for crustose seaweeds. We experimentally validated the effect of host morphology by quantifying bacterial community assembly on latex sheets cut to resemble three seaweed morphologies. The patterns match those observed in our field survey. Thus, biodiversity increases with habitat complexity in host-associated microbial communities, mirroring patterns observed in animal communities. We suggest that host morphology and structural complexity are underexplored mechanisms structuring microbial communities.
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143
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Greslehner GP. Not by structures alone: Can the immune system recognize microbial functions? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2020; 84:101336. [PMID: 32830048 DOI: 10.1016/j.shpsc.2020.101336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
A central question for immunology is: what does the immune system recognize and according to which principles does this kind of recognition work? Immunology has been dominated by the idea of recognizing molecular structures and triggering an appropriate immune response when facing non-self or danger. Recently, characterizations in terms of function have turned out to be more conserved and explanatory in microbiota research than taxonomic composition for understanding microbiota-host interactions. Starting from a conceptual analysis of the notions of structure and function, I raise the title question whether it is possible for the immune system to recognize microbial functions. I argue that this is indeed the case, making the claim that some function-associated molecular patterns are not indicative of the presence of certain taxa (''who is there'') but of biochemical activities and effects (''what is going on''). In addition, I discuss case studies which show that there are immunological sensors that can directly detect microbial activities, irrespective of their specific structural manifestation. At the same time, the discussed account puts the causal role notions of function on a more realist and objective basis.
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Affiliation(s)
- Gregor P Greslehner
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, 33076, Bordeaux, France.
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144
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Ihua MW, FitzGerald JA, Guihéneuf F, Jackson SA, Claesson MJ, Stengel DB, Dobson ADW. Diversity of bacteria populations associated with different thallus regions of the brown alga Laminaria digitata. PLoS One 2020; 15:e0242675. [PMID: 33237941 PMCID: PMC7688147 DOI: 10.1371/journal.pone.0242675] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/08/2020] [Indexed: 12/20/2022] Open
Abstract
Stipitate kelp species such as Laminaria digitata dominate most cold-water subtidal rocky shores and form underwater forests which are among the most productive coastal systems worldwide. Laminaria also sustains rich bacterial communities which offer a variety of biotechnological applications. However, to date, in-depth studies on the diversity and uniqueness of bacterial communities associated with this macroalgal species, their ecological role and their interactions with the alga are under-represented. To address this, the epibacterial populations associated with different thallus regions (holdfast, stipe, meristem, blade) of this brown seaweed were investigated using high-throughput Illumina sequencing of the 16S rRNA genes. The results show that epibacterial communities of the brown seaweed are significantly different and specific to the thallus region, with the shared bacterial population comprising of only 1.1% of the total amplicon sequence variants. The diverse holdfast and blade tissues formed distinct clusters while the meristem and stipe regions are more closely related. The data obtained further supports the hypothesis that macroalgal bacterial communities are shaped by morphological niches and display specificity.
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Affiliation(s)
- Maureen W. Ihua
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jamie A. FitzGerald
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Dagmar B. Stengel
- Botany and Plant Science, School of Natural Sciences, Ryan Institute for Environmental, Marine and Energy Research, National University of Ireland Galway, Galway, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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145
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Estrada-Peña A, Cabezas-Cruz A, Obregón D. Behind Taxonomic Variability: The Functional Redundancy in the Tick Microbiome. Microorganisms 2020; 8:microorganisms8111829. [PMID: 33233565 PMCID: PMC7699746 DOI: 10.3390/microorganisms8111829] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/30/2022] Open
Abstract
The taxonomic composition and diversity of tick midgut microbiota have been extensively studied in different species of the genera Rhipicephalus, Ixodes, Amblyomma, Haemaphysalis, Hyalomma, Dermacentor, Argas and Ornithodoros, while the functional significance of bacterial diversity has been proportionally less explored. In this study, we used previously published 16S amplicon sequence data sets from three Ixodes scapularis cohorts, two of uninfected nymphs, and one of larvae experimentally infected with Borrelia burgdorferi, to test the functional redundancy of the tick microbiome. We predicted the metabolic profiling of each sample using the state-of-the-art metagenomics tool PICRUSt2. The results showed that the microbiomes of all I. scapularis samples share only 80 taxa (24.6%, total 324), while out of the 342 metabolic pathways predicted, 82.7%, were shared by all the ticks. Borrelia-infected larvae lack 15.4% of pathways found in the microbiome of uninfected nymphs. Taxa contribution analysis showed that the functional microbiome of uninfected ticks was highly redundant, with, in some cases, up to 198 bacterial taxa contributing to a single pathway. However, Borrelia-infected larvae had a smaller redundancy with 6.7% of pathways provided by more than 100 genera, while 15.7–19.2% of pathways were provided by more than 100 genera in the two cohorts of uninfected ticks. In addition, we compared the functional profiles of three microbial communities from each data set, identified through a network-based approach, and we observed functional similarity between them. Based on the functional redundancy and functional similarity of the microbiome of ticks in different developmental stages and infection status, we concluded that the tick gut microbiota is a self-regulating community of very diverse bacteria contributing to a defined set of metabolic pathways and functions with yet unexplored relevance for tick fitness and/or bacterial community stability. We propose a change of focus in which the tick microbiome must be analyzed in all dimensions, highlighting their functional traits, instead of the conventional taxonomic profiling.
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Affiliation(s)
- Agustín Estrada-Peña
- Faculty of Veterinary Medicine, University of Zaragoza, 50013 Zaragoza, Spain
- Correspondence: (A.E.-P.); (D.O.)
| | - Alejandro Cabezas-Cruz
- UMR BIPAR, INRAE, ANSES, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France;
| | - Dasiel Obregón
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, São Paulo 13400-970, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence: (A.E.-P.); (D.O.)
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146
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Renoud S, Bouffaud ML, Dubost A, Prigent-Combaret C, Legendre L, Moënne-Loccoz Y, Muller D. Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere. FEMS Microbiol Ecol 2020; 96:5818760. [PMID: 32275303 DOI: 10.1093/femsec/fiaa062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.
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Affiliation(s)
- Sébastien Renoud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Marie-Lara Bouffaud
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Laurent Legendre
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France.,Univ Lyon, Université de St Etienne, 10, Rue Tréfilerie - F-42023 Saint-Etienne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
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147
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Stencel A. Do seasonal microbiome changes affect infection susceptibility, contributing to seasonal disease outbreaks? Bioessays 2020; 43:e2000148. [PMID: 33165975 DOI: 10.1002/bies.202000148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
The aim of the present paper is to explore whether seasonal outbreaks of infectious diseases may be linked to changes in host microbiomes. This is a very important issue, because one way to have more control over seasonal outbreaks is to understand the factors that underlie them. In this paper, I will evaluate the relevance of the microbiome as one of such factors. The paper is based on two pillars of reasoning. Firstly, on the idea that microbiomes play an important role in their hosts' defence against infectious diseases. Secondly, on the idea that microbiomes are not stable, but change seasonally. These two ideas are combined in order to argue that seasonal changes in a given microbiome may influence the functionality of the host's immune system and consequently make it easier for infectious agents to infect the host at certain times of year. I will argue that, while this is only a theoretical possibility, certain studies may back up such claims. Furthermore, I will show that this does not necessarily contradict other hypotheses aimed at explaining seasonal outbreaks; in fact, it may even enhance them.
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Affiliation(s)
- Adrian Stencel
- Institute of Philosophy, Jagiellonian University, Kraków, Poland
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148
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Louca S, Rubin IN, Madilao LL, Bohlmann J, Doebeli M, Wegener Parfrey L. Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:514-524. [PMID: 32618124 DOI: 10.1111/1758-2229.12866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Ilan N Rubin
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Lufiani L Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
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149
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Grajal-Puche A, Murray CM, Kearley M, Merchant M, Nix C, Warner JK, Walker DM. Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales. MICROBIAL ECOLOGY 2020; 80:603-613. [PMID: 32424717 DOI: 10.1007/s00248-020-01522-9] [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: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.
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Affiliation(s)
| | - Christopher M Murray
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70402, USA
- Biology Department, Tennessee Technological University, Cookeville, TN, 38505, USA
| | - Matthew Kearley
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mark Merchant
- Department of Chemistry, McNeese State University, Lake Charles, LA, 70609, USA
| | - Christopher Nix
- Alabama Wildlife and Freshwater Fisheries Division, Montgomery, AL, 36130, USA
| | | | - Donald M Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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150
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Lam TJ, Stamboulian M, Han W, Ye Y. Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput Biol 2020; 16:e1007951. [PMID: 33125363 PMCID: PMC7657538 DOI: 10.1371/journal.pcbi.1007951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/11/2020] [Accepted: 09/10/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial community members exhibit various forms of interactions. Taking advantage of the increasing availability of microbiome data, many computational approaches have been developed to infer bacterial interactions from the co-occurrence of microbes across diverse microbial communities. Additionally, the introduction of genome-scale metabolic models have also enabled the inference of cooperative and competitive metabolic interactions between bacterial species. By nature, phylogenetically similar microbial species are more likely to share common functional profiles or biological pathways due to their genomic similarity. Without properly factoring out the phylogenetic relationship, any estimation of the competition and cooperation between species based on functional/pathway profiles may bias downstream applications. To address these challenges, we developed a novel approach for estimating the competition and complementarity indices for a pair of microbial species, adjusted by their phylogenetic distance. An automated pipeline, PhyloMint, was implemented to construct competition and complementarity indices from genome scale metabolic models derived from microbial genomes. Application of our pipeline to 2,815 human-gut associated bacteria showed high correlation between phylogenetic distance and metabolic competition/cooperation indices among bacteria. Using a discretization approach, we were able to detect pairs of bacterial species with cooperation scores significantly higher than the average pairs of bacterial species with similar phylogenetic distances. A network community analysis of high metabolic cooperation but low competition reveals distinct modules of bacterial interactions. Our results suggest that niche differentiation plays a dominant role in microbial interactions, while habitat filtering also plays a role among certain clades of bacterial species.
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Affiliation(s)
- Tony J. Lam
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Moses Stamboulian
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Wontack Han
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- Luddy School of Informatics, Computing and Engineering Indiana University, Bloomington, IN, USA
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