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Wang Y, Zheng G, Zhao Y, Bo H, Li C, Dong J, Wang Y, Yan S, Zhang F, Liu J. Different bacterial and fungal community patterns in restored habitats in coal-mining subsidence areas. Environ Sci Pollut Res Int 2023; 30:104304-104318. [PMID: 37700132 DOI: 10.1007/s11356-023-29744-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/03/2023] [Indexed: 09/14/2023]
Abstract
Soil microbiota, which plays a fundamental role in ecosystem functioning, is sensitive to environmental changes. Studying soil microbial ecological patterns can help to understand the consequences of environmental disturbances on soil microbiota and hence ecosystem services. The different habitats with critical environmental gradients generated through the restoration of coal-mining subsidence areas provide an ideal area to explore the response of soil microbiota to environmental changes. Here, based on high-throughput sequencing, we revealed the patterns of soil bacterial and fungal communities in habitats with different land-use types (wetland, farmland, and grassland) and with different restored times which were generated during the ecological restoration of a typical coal-mining subsidence area in Jining City, China. The α-diversity of bacterial was higher in wetland than in farmland and grassland, while that of fungi had no discrepancy among the three habitats. The β-diversity of bacterial community in the grassland was lower than in the farmland, and fungal community was significant different in all three habitats, showing wetland, grassland, and farmland from high to low. The β-diversity of the bacterial community decreased with restoration time while that of the fungal community had no significant change in the longer-restoration-time area. Furthermore, soil electrical conductivity was the most important driver for both bacterial and fungal communities. Based on the taxonomic difference among different habitats, we identified a group of biomarkers for each habitat. The study contributes to understand the microbial patterns during the ecological restoration of coal-mining subsidence areas, which has implications for the efficient ecological restoration of subsidence areas.
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Affiliation(s)
- Yijing Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Guodong Zheng
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China.
| | - Yongkang Zhao
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Huaizhi Bo
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China
| | - Changchao Li
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Junyu Dong
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Yan Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Shuwan Yan
- Environment Research Institute, Shandong University, Qingdao, 266237, China
| | - Fanglong Zhang
- Technology Innovation Center of Restoration and Reclamation in Mining induced Subsidence Land, Ministry of Natural Resources, Shandong Provincial Lunan Geology and Exploration Institute (Shandong Provincial Bureau of Geology and Mineral Resources No.2 Geological Brigade), Jining, 272000, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao, 266237, China
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Enns D, Cunze S, Baker NJ, Oehlmann J, Jourdan J. Flushing away the future: The effects of wastewater treatment plants on aquatic invertebrates. Water Res 2023; 243:120388. [PMID: 37517151 DOI: 10.1016/j.watres.2023.120388] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Wastewater treatment plants (WWTP) are essential infrastructure in our developing world. However, with the development and release of novel entities and without modern upgrades, they are ineffective at fully removing micropollutants before treated effluents are released back into aquatic environments. Thus, WWTPs may represent additional point source impacts to freshwater environments, further pressuring aquatic fauna and already vulnerable insect communities. Previous studies - mostly focusing on single WWTPs - have shown general trends of freshwater invertebrate communities becoming dominated by pollution tolerant taxa. To expand on these findings, the current study is the first to comprehensively investigate data on the effects of 170 WWTPs on invertebrate taxonomic composition. We compared data for several diversity and pollution indices, as well as the taxonomic composition both upstream and downstream of the WWTPs (366 sampling sites). In terms of abundance, the three most frequent and negatively impacted orders were the Plecoptera, Trichoptera and Gastropoda, while the Turbellaria, Hirudinea and Crustacea increased in abundance. Although strong changes in community composition were observed between upstream and downstream sites (mean species turnover of 61%), commonly used diversity indices were not sensitive to these changes, highlighting their potential inadequacy in accurately assessing ecological health. Our results indicate that WWTPs change downstream conditions in favour of pollution tolerant taxa to the detriment of sensitive taxa. Order-level taxonomic responses can be informative but should be interpreted with caution, since they can be driven by a few taxa, or opposing responses of species in the same group can result in an overall low order-level response. Upgrading WWTPs via additional treatment steps or merging may be beneficial, provided upstream sections are unimpacted and/or are in a good chemical and structural condition.
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Affiliation(s)
- Daniel Enns
- Goethe University Frankfurt, Department Aquatic Ecotoxicology, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany; Kompetenzzentrum Wasser Hessen, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany.
| | - Sarah Cunze
- Goethe University Frankfurt, Department of Integrative Parasitology and Zoophysiology, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany
| | - Nathan Jay Baker
- Nature Research Centre, Institute of Ecology, Akademijos Str. 2, LT-08412 Vilnius, Lithuania
| | - Jörg Oehlmann
- Goethe University Frankfurt, Department Aquatic Ecotoxicology, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany; Kompetenzzentrum Wasser Hessen, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany
| | - Jonas Jourdan
- Goethe University Frankfurt, Department Aquatic Ecotoxicology, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany; Kompetenzzentrum Wasser Hessen, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany.
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Bao Y, Chen Y, Wang F, Xu Z, Zhou S, Sun R, Wu X, Yan K. East Asian monsoon manipulates the richness and taxonomic composition of airborne bacteria over China coastal area. Sci Total Environ 2023; 875:162581. [PMID: 36889406 DOI: 10.1016/j.scitotenv.2023.162581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Airborne bacteria may have significant impacts on aerosol properties, public health and ecosystem depending on their taxonomic composition and transport. This study investigated the seasonal and spatial variations of bacterial composition and richness over the east coast of China and the roles of East Asian monsoon played through synchronous sampling and 16S rRNA sequencing analysis of airborne bacteria at Huaniao island of the East China Sea (ECS) and the urban and rural sites of Shanghai. Airborne bacteria showed higher richness over the land sites than Huaniao island with the highest values found in the urban and rural springs associated with the growing plants. For the island, the maximal richness occurred in winter as the result of prevailing terrestrial winds controlled by East Asian winter monsoon. Proteobacteria, Actinobacteria and Cyanobacteria were found to be top three phyla, together accounting for 75 % of total airborne bacteria. Radiation-resistant Deinococcus, Methylobacterium belonging to Rhizobiales (related to vegetation) and Mastigocladopsis_PCC_10914 originating from marine ecosystem were indicator genera for urban, rural and island sites, respectively. The Bray-Curits dissimilarity of taxonomic composition between the island and two land sites was the lowest in winter with the representative genera over island also typically from the soil. Our results reveal that seasonal change of monsoon wind directions evidently affects the richness and taxonomic composition of airborne bacteria in China coastal area. Particularly, prevailing terrestrial winds lead to the dominance of land-derived bacteria over the coastal ECS which may have a potential impact on marine ecosystem.
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Affiliation(s)
- Yang Bao
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ying Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China; Institute of Eco-Chongming (IEC), National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Shanghai 202162, China.
| | - Fanghui Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Zongjun Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Shengqian Zhou
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ruihua Sun
- Pudong New District Environmental Monitoring Station, Shanghai 200135, China
| | - Xiaowei Wu
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Ke Yan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
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Hua E, He L, Zhang Z, Cui C, Liu X. Bioassessment of environmental quality based on taxonomic and functional traits of marine nematodes in the Bohai Sea, China. Mar Pollut Bull 2023; 190:114884. [PMID: 37011536 DOI: 10.1016/j.marpolbul.2023.114884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Free-living marine nematodes are valuable biological indicators for different environmental disturbances. Their taxonomic composition and functional traits often respond to environmental changes. In this study, marine nematodes, collected from the Bohai sea on the northeastern coast of China in 2014, were investigated in terms of their taxonomic composition and functional traits. Furthermore, the environmental quality of the investigated area was assessed based on nematode metrics. The studied nematode community showed spatial variation in taxonomic and functional composition, in response to changes in environmental variables such as sediment chlorophyll-a, phaeophytin-a, organic matter content, silt-clay content etc. Overall, high percentage of tolerant marine nematodes species or colonizers predominated, suggesting a disturbed environmental condition of the study area. Further results from the environmental quality assessment based on nematode metrics indicated a moderate quality status at the most investigated stations.
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Affiliation(s)
- Er Hua
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Lei He
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Zhinan Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chunyan Cui
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Xiaoshou Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Carneiro de Melo Moura C, Setyaningsih CA, Li K, Merk MS, Schulze S, Raffiudin R, Grass I, Behling H, Tscharntke T, Westphal C, Gailing O. Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra. BMC Ecol Evol 2022; 22:51. [PMID: 35473550 PMCID: PMC9040256 DOI: 10.1186/s12862-022-02004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intense conversion of tropical forests into agricultural systems contributes to habitat loss and the decline of ecosystem functions. Plant-pollinator interactions buffer the process of forest fragmentation, ensuring gene flow across isolated patches of forests by pollen transfer. In this study, we identified the composition of pollen grains stored in pot-pollen of stingless bees, Tetragonula laeviceps, via dual-locus DNA metabarcoding (ITS2 and rbcL) and light microscopy, and compared the taxonomic coverage of pollen sampled in distinct land-use systems categorized in four levels of management intensity (forest, shrub, rubber, and oil palm) for landscape characterization. RESULTS Plant composition differed significantly between DNA metabarcoding and light microscopy. The overlap in the plant families identified via light microscopy and DNA metabarcoding techniques was low and ranged from 22.6 to 27.8%. Taxonomic assignments showed a dominance of pollen from bee-pollinated plants, including oil-bearing crops such as the introduced species Elaeis guineensis (Arecaceae) as one of the predominant taxa in the pollen samples across all four land-use types. Native plant families Moraceae, Euphorbiaceae, and Cannabaceae appeared in high proportion in the analyzed pollen material. One-way ANOVA (p > 0.05), PERMANOVA (R² values range from 0.14003 to 0.17684, for all tests p-value > 0.5), and NMDS (stress values ranging from 0.1515 to 0.1859) indicated a lack of differentiation between the species composition and diversity of pollen type in the four distinct land-use types, supporting the influx of pollen from adjacent areas. CONCLUSIONS Stingless bees collected pollen from a variety of agricultural crops, weeds, and wild plants. Plant composition detected at the family level from the pollen samples likely reflects the plant composition at the landscape level rather than the plot level. In our study, the plant diversity in pollen from colonies installed in land-use systems with distinct levels of forest transformation was highly homogeneous, reflecting a large influx of pollen transported by stingless bees through distinct land-use types. Dual-locus approach applied in metabarcoding studies and visual pollen identification showed great differences in the detection of the plant community, therefore a combination of both methods is recommended for performing biodiversity assessments via pollen identification.
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Affiliation(s)
| | - Christina A Setyaningsih
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Kevin Li
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Miryam Sarah Merk
- Statistics and Econometrics, University of Göttingen, Göttingen, Germany
| | - Sonja Schulze
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Rika Raffiudin
- Department of Biology, IPB University ID, Bogor, West Java, 16880, Indonesia
| | - Ingo Grass
- Department of Ecology of Tropical Agricultural Systems, University of Hohenheim, 70599, Stuttgart, Germany
| | - Hermann Behling
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Teja Tscharntke
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Catrin Westphal
- Functional Agrobiodiversity, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany. .,Centre of Biodiversity and Sustainable Land Use, University of Göttingen, 37077, Göttingen, Germany.
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Narita Y, Kodama H. Identification of the specific microbial community compositions in saliva associated with periodontitis during pregnancy. Clin Oral Investig 2022. [PMID: 35352183 DOI: 10.1007/s00784-022-04468-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/17/2022] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To identify the specific microbial community compositions in saliva associated with periodontitis during pregnancy. MATERIALS AND METHODS Unstimulated saliva samples were collected from 53 pregnant women during weeks 24-28 of gestation, and the V3-V4 regions of the 16S rRNA gene were amplified from isolated saliva DNA and sequenced. Phylum-, genus-, and species-level taxonomic compositions were separately compared between subjects with (n = 12) and without (n = 41) periodontitis. RESULTS Taxa were selected using the random forest algorithm to distinguish subjects with periodontitis at each taxonomic level, and principal component biplots were constructed to visualize the composition of selected taxa in each subject. The genus-level biplot indicated that 44 subjects clustered around the origin. The prevalence of periodontitis was significantly higher among subjects outside the cluster compared with subjects inside the cluster (6/9 [67%] vs. 6/44 [14%], respectively; p = 0.002). Subjects outside the cluster also had significantly decreased abundance of Neisseria and increased abundances of several putative periodontopathic genera. Phylum- and species-level biplots failed to discriminate subjects with periodontitis more efficiently than the genus-level biplot. CONCLUSIONS The specific taxonomic composition of the saliva microbiota in pregnant women with periodontitis could be clearly identified at the genus level. CLINICAL RELEVANCE The formula developed based on the present findings, (%Treponema + %Tannerella + %Filifactor + %Anaeroglobus)/%Neisseria, can be used to predict periodontitis during pregnancy with sensitivity and specificity values of 0.67 (8/12) and 0.95 (39/41), respectively.
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Sharma Ghimire P, Joshi DR, Tripathee L, Chen P, Sajjad W, Kang S. Seasonal taxonomic composition of microbial communal shaping the bioaerosols milieu of the urban city of Lanzhou. Arch Microbiol 2022; 204:222. [PMID: 35344106 DOI: 10.1007/s00203-022-02832-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
Abstract
Here, the taxonomical composition and seasonal dynamics of airborne microbial communities were described in the urban city of Lanzhou, Northwest China. Year-long samples were studied in two filter membranes (Quartz and PTFE). Higher microbial loads were reported in the PTFE than in the quartz filter. Onefold decrease was reported in bacterial loads in spring and summer than winter and autumn for both filters. The fungal loadings were lowest during winter and highest during autumn, followed by summer. The microbial communities included Actinobacteria and Proteobacteria, Ascomycota, and Basidiomycota as major components. Maximum abundance of the members from Gammaproteobacteria, Coriobacteria and Clostridia were studied in all seasons on PTFE membrane, followed by, Erysipelotrichia, Negativicutes and Fusobacteria. Members of Actinobacteria and Bacilli showed higher abundance in spring and winter, with a small proportion during autumn. Members of Clostridia, Gammaproteobacteria, Bacilli, and Actinobacteria showed maximum abundance on the quartz filter in all the seasons. Similarly, on the PTFE, fungi including Dothideomycetes and Agaricomycetes were dominant, followed by Saccharomycetes during summer and winter. The result showed that PM2.5, SO42-, NO2-, Na+, EC, and OC are important environmental parameters influencing the seasonal microbial community. However, the relation of the microbiome with the environment cannot be confidently defined because the environmental factors are changeable and yet interrelated.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China.,Himalayan Environment Research Institute (HERI), Kathmandu, 44602, Nepal
| | - Dev Raj Joshi
- Central Department of Microbiology, Tribhuvan University, Kirtipur, 44613, Nepal
| | - Lekhendra Tripathee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China.,Himalayan Environment Research Institute (HERI), Kathmandu, 44602, Nepal
| | - Pengfei Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China
| | - Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China. .,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, 100085, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100864, People's Republic of China.
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Borjigin Q, Zhang B, Yu X, Gao J, Zhang X, Qu J, Ma D, Hu S, Han S. Metagenomics study to compare the taxonomic composition and metabolism of a lignocellulolytic microbial consortium cultured in different carbon conditions. World J Microbiol Biotechnol 2022; 38:78. [PMID: 35325312 DOI: 10.1007/s11274-022-03260-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
A lignocellulolytic microbial consortium holds promise for the in situ biodegradation of crop straw and the comprehensive and effective utilization of agricultural waste. In this study, we applied metagenomics technology to comprehensively explore the metabolic functional potential and taxonomic diversity of the microbial consortia CS (cultured on corn stover) and FP (cultured on filter paper). Analyses of the data on metagenomics taxonomic affiliations revealed considerable differences in the taxonomic composition and carbohydrate-active enzymes profile of the microbial consortia CS and FP. Pseudomonas, Dysgonomonas and Sphingobacterium in CS and Cellvibrio and Pseudomonas in FP had a much wider distribution of lignocellulose degradative ability. The genes for more lignocellulose degradative enzymes were detected when the relatively simple substrate filter paper was used as the carbon source. Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses revealed considerable levels of similarity, and carbohydrate metabolic and amino acid metabolic pathways were the most enriched in CS and FP, respectively. The mechanism used by the two microbial consortia to degrade lignocellulose was similar, but the annotation of quantity of genes indicated that they are diverse and vary greatly. These data underlie the interactions between microorganisms and the synergism of enzymes during the degradative process of lignocellulose under different substrates and suggest the development of potential microbial resources.
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Affiliation(s)
- Qinggeer Borjigin
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Bizhou Zhang
- Special Crops Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, No.22, ZhaoJun Road, Hohhot, 010031, China
| | - Xiaofang Yu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Julin Gao
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China. .,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.
| | - Xin Zhang
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Jiawei Qu
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Daling Ma
- Agricultural College, Inner Mongolia Agricultural University, No. 275, XinJian East Street, Hohhot, 010019, China.,Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China
| | - Shuping Hu
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Vocational and Technical College, Inner Mongolia Agricultural University, Altan street, Baotou, 014109, China
| | - Shengcai Han
- Key Laboratory of Crop Cultivation and Genetic Improvement in Inner Mongolia Autonomous Region, No. 275, XinJian East Street, Hohhot, 010019, China.,Hortlculture and Plant Protection College, Inner Mongolia Agricultural University, No. 29, Eerduosi East Street, Hohhot, 010019, China
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Lima J, Manning T, Rutherford KM, Baima ET, Dewhurst RJ, Walsh P, Roehe R. Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. J Microbiol Methods 2021; 186:106235. [PMID: 33974954 DOI: 10.1016/j.mimet.2021.106235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/04/2023]
Abstract
Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.
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Allouche M, Nasri A, Harrath AH, Mansour L, Alwasel S, Beyrem H, Plăvan G, Rohal-Lupher M, Boufahja F. Do presence of gray shrimp Crangon crangon larvae influence meiobenthic features? Assessment with a focus on traits of nematodes. Environ Sci Pollut Res Int 2021; 28:21303-21313. [PMID: 33411276 DOI: 10.1007/s11356-020-12069-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
In this study, a microcosm experiment was conducted for 30 days to assess the impact of the presence of juvenile gray shrimp Crangon crangon on meiofauna. The results suggested that juvenile shrimp had a significant negative impact on the abundance of nematodes and copepods, but no effect on polychaetes. Moreover, nematodes showed a significant decline in individual weight. The collected nematodes were taxonomically identified and assigned to five functional traits: shapes of the tail and amphid, life history, feeding types, and adult length. The nematode traits were affected by the number of shrimp introduced, and descriptors followed normal or inversed bell-shaped curves. When no shrimp were present, the nematofauna had a higher species richness compared with treatments of 4, 8, and 12 shrimp. Bell-shaped curve patterns were common in relation to the two phases of feeding for C. crangon. During the first phase, C. crangon consumed the nematode species Oncholaimus campylocercoides; thereafter, shrimp fed mostly on the nematode Anticoma eberthi and copepods.
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Affiliation(s)
- Mohamed Allouche
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Ahmed Nasri
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Abdel Halim Harrath
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Lamjed Mansour
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Saleh Alwasel
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hamouda Beyrem
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Gabriel Plăvan
- Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - Melissa Rohal-Lupher
- Texas Water Development Board, 1700 North Congress Avenue, Austin, TX, 78701, USA
| | - Fehmi Boufahja
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia.
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11
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Rifkin RF, Vikram S, Ramond JB, Rey-Iglesia A, Brand TB, Porraz G, Val A, Hall G, Woodborne S, Le Bailly M, Potgieter M, Underdown SJ, Koopman JE, Cowan DA, Van de Peer Y, Willerslev E, Hansen AJ. Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome. Microbiome 2020; 8:62. [PMID: 32375874 PMCID: PMC7204047 DOI: 10.1186/s40168-020-00832-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/18/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen. METHODS Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM. RESULTS Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants. CONCLUSIONS Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.
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Affiliation(s)
- Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Tina B Brand
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
| | - Guillaume Porraz
- CNRS, UMR 7041 ArScAn-AnTET, Université Paris-Nanterre, Paris, France
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
| | - Aurore Val
- Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein Johannesburg, South Africa
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Stephan Woodborne
- Mammal Research Institute, University of Pretoria, Hatfield, South Africa
- iThemba LABS, Braamfontein Johannesburg, South Africa
| | - Matthieu Le Bailly
- University of Bourgogne France-Comte, CNRS UMR 6249 Chrono-environment, Besancon, France
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Yves Van de Peer
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- VIB Centre for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Eske Willerslev
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anders J Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Hatfield, Denmark.
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12
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Zhai Y, Hunting ER, Liu G, Baas E, Peijnenburg WJGM, Vijver MG. Compositional alterations in soil bacterial communities exposed to TiO 2 nanoparticles are not reflected in functional impacts. Environ Res 2019; 178:108713. [PMID: 31518961 DOI: 10.1016/j.envres.2019.108713] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 05/23/2023]
Abstract
Titanium dioxide nanoparticles (TiO2NP) are increasingly released in soil ecosystems, while there is limited understanding of the impacts of TiO2NP on soil bacterial communities. Here we investigated the effects of TiO2NP on the taxonomic composition and functional profile of a soil bacterial community over a 60-day exposure period. In short-term exposure (1-day), contradictory effects on the taxonomic composition of soil bacterial communities were found after exposure to a low realistic environmental concentration of TiO2NP at 1 mg/kg as compared to the effects induced by medium and high concentrations of TiO2NP at 500 and 2000 mg/kg. After long-term exposure (60-day), the negative effects of TiO2NP at the low concentration disappeared, and the inhibition by TiO2NP of the abundance of core taxa was enhanced along with increasing exposure concentrations. However, although significant alterations were observed in the taxonomic composition over time and exposure concentrations, no significant change was observed in the community functional profile as well as enzyme activity after 60-day exposure, indicating that functional redundancy likely contributed to the bacterial community tolerance after the exposure to TiO2NP. Our study highlighted the importance of assessing bacterial community compositional and functional responses in assessing the environmental risk of nanoparticles on soil ecosystems.
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Affiliation(s)
- Yujia Zhai
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands.
| | - Ellard R Hunting
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Gang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China; Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600GA, Delft, the Netherlands.
| | - Elise Baas
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands; National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300, RA, Leiden, the Netherlands
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13
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van der Linden P, Shinn C, Moreira-Santos M, Oehlmann J, Ribeiro R, Müller R. Aquatic mesocosms exposed to a fungicide in warm and cold temperate European climate zones: Long-term macroinvertebrate response. Sci Total Environ 2019; 681:133-142. [PMID: 31103651 DOI: 10.1016/j.scitotenv.2019.05.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
At present, the European Union legislation facilitates the use of similar pesticides among European Member States, thereby assuming that biodiversity and ecosystems have equal sensitivities to contaminants throughout the whole of Europe. However, with this assumption, fundamental environmental and biological differences between climatic zones are being ignored in Environmental Risk Assessment. Such differences may strongly influence the behaviour of contaminants, their effects on biodiversity and on the natural functioning of ecosystems. Furthermore, toxicity testing in European ecoregions other than cold-temperate has largely depended on standardized tests using cold-temperate species and conditions, which may lead to a false estimation of risks to organisms from other ecoregions. The present study aim was to determine the response of freshwater macroinvertebrate communities to the fungicide pyrimethanil by conducting aquatic mesocosm experiments in two different ecoregions with different climates: cold-temperate (Frankfurt, Germany) and warm-temperate (Coimbra, Portugal). The results indicate that the community in the cold-temperate climate was more sensitive to the fungicide in comparison to the warm-temperate community. This difference was most likely related to a different rate of fungicide disappearance, which was slower in the colder climate. Based upon our results we discuss important implications for improving Environmental Risk Assessment across climate zones and under present-day global climate change scenarios.
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Affiliation(s)
- P van der Linden
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| | - C Shinn
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal
| | - M Moreira-Santos
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal
| | - J Oehlmann
- Goethe University, Department Aquatic Ecotoxicology, Max von Laue straße 13, Frankfurt 60438, Germany
| | - R Ribeiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal
| | - R Müller
- Goethe University, Institute of Occupational Social and Environmental Medicine, Theodor Stern Kai 7, Frankfurt 60590, Germany; Institute of Tropical Medicine, Nationalestraat 155, Antwerp 2000, Belgium
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14
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Li Z, Wang J, Liu Z, Meng X, Heino J, Jiang X, Xiong X, Jiang X, Xie Z. Different responses of taxonomic and functional structures of stream macroinvertebrate communities to local stressors and regional factors in a subtropical biodiversity hotspot. Sci Total Environ 2019; 655:1288-1300. [PMID: 30577121 DOI: 10.1016/j.scitotenv.2018.11.222] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Examining the relative contribution of local environmental stressors and regional factors in structuring biological communities is essential for biodiversity conservation and environmental assessment, yet their relative roles for different community characterizations remain elusive. Here, we examined the responses of taxonomic and functional structures of stream macroinvertebrate communities to local and regional factors across a human-induced environmental gradient in the Han River Basin, one subtropical biodiversity hotspot in China. Our objectives were: 1) to examine the responses of traditional taxonomic measures and functional traits to anthropogenic disturbances; 2) to compare the relative importance of environmental versus spatial variables and catchment-scale versus reach-scale variables for the two community characterizations. We found that both species and trait compositions performed well in differentiating anthropogenic disturbances, indicating that both taxonomic and functional structures of macroinvertebrate communities were strongly altered by human activities. Particularly, some traits related to life history (e.g., voltinism), resilience and resistance (e.g., adult flying ability) are well suited for predicting changes of communities towards anthropogenic disturbances owing to their mechanistic relationship with environmental gradients. We found that environmental variables played more important roles than spatial effects in structuring both taxonomic and functional facets of macroinvertebrate communities. Environmental filtering was more important in determining functional than taxonomic structure, and the opposite was true for spatial effects. In terms of environmental variables, catchment land-uses played the primary role in determining taxonomic composition, whereas reach-scale variables related to local habitat heterogeneity were more influential for functional structure. Our study highlights the importance of employing metacommunity perspectives and different community characterizations in both theoretical and applied research. For stream bioassessment and management, we argue that the combination of taxonomic and functional characterizations of community should be implemented, as different facets of biological communities responded to different types of anthropogenic disturbances.
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Affiliation(s)
- Zhengfei Li
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jun Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Zhenyuan Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xingliang Meng
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jani Heino
- Biodiversity Centre, Finnish Environment Institute, Paavo Havaksen Tie 3, P.O. Box 413, 90014 Oulu, Finland.
| | - Xuankong Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiong Xiong
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Xiaoming Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China.
| | - Zhicai Xie
- The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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15
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Lemes da Silva AL, Petrucio MM. Relationships between aquatic invertebrate communities, water-level fluctuations and different habitats in a subtropical lake. Environ Monit Assess 2018; 190:548. [PMID: 30143869 DOI: 10.1007/s10661-018-6929-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/14/2018] [Indexed: 06/08/2023]
Abstract
In lakes, the littoral habitat and its invertebrate communities are often exposed to water-level fluctuations. We examined the effects of seasonal changes on water level, substrata availability and benthic fauna in the littoral zone of Peri Lake, a shallow lake that has experienced a strong reduction in water level due to changes in rainfall. In this study, we also examined whether the abundance and composition of aquatic invertebrates differed among the four substrata. Our main objective was to assess the effect of seasonal changes on water level and benthic invertebrates inhabiting the different types of substrata. Benthic invertebrates were sampled four different substrata (Schoenoplectus californicus, sand and stones, allochthonous leaf litter, and macrophyte stands), and we also measured meteorological, physical and chemical variables. We found that complex habitats, such as allochthonous leaf litter and aquatic macrophyte, stand to be colonised by a larger number of macroinvertebrates because they provide more habitats or potential niches for colonisation by different species. In addition, we observed that during periods of low water level, the presence of substrata in the littoral zone decreased, as did the associated biota. Therefore, our results suggest that water level changes have a major functional impact on the littoral zone of the lake, and can affect substratum availability, which also impacts invertebrate communities.
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Affiliation(s)
- Aurea Luiza Lemes da Silva
- Laboratório de Ecologia de Águas Continentais, Programa de Pós-Graduação em Ecologia, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil.
| | - Mauricio Mello Petrucio
- Laboratório de Ecologia de Águas Continentais, Programa de Pós-Graduação em Ecologia, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil
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16
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Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K. VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. BMC Syst Biol 2018; 12:30. [PMID: 29560821 PMCID: PMC5861490 DOI: 10.1186/s12918-018-0545-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes’ phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities. Results We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community. Conclusions The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing. Electronic supplementary material The online version of this article (10.1186/s12918-018-0545-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroshi Mori
- Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Takayuki Maruyama
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masahiro Yano
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takuji Yamada
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
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17
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He J, Tu Q, Ge Y, Qin Y, Cui B, Hu X, Wang Y, Deng Y, Wang K, Van Nostrand JD, Li J, Zhou J, Li Y, Zhou X. Taxonomic and Functional Analyses of the Supragingival Microbiome from Caries-Affected and Caries-Free Hosts. Microb Ecol 2018; 75:543-554. [PMID: 28932895 DOI: 10.1007/s00248-017-1056-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Caries is one of the most prevalent and costly infectious diseases affecting humans of all ages. It is initiated by cariogenic supragingival dental plaques forming on saliva-coated tooth surfaces, yet the etiology remains elusive. To determine which microbial populations may predispose a patient to caries, we report here an in-depth and comprehensive view of the microbial community associated with supragingival dental plaque collected from the healthy teeth of caries patients and healthy adults. We found that microbial communities from caries patients had a higher evenness and inter-individual variations but simpler ecological networks compared to healthy controls despite the overall taxonomic structure being similar. Genera including Selenomonas, Treponema, Atopobium, and Bergeriella were distributed differently between the caries and healthy groups with disturbed co-occurrence patterns. In addition, caries and healthy subjects carried different Treponema, Atopobium, and Prevotella species. Moreover, distinct populations of 13 function genes involved in organic acid synthesis, glycan biosynthesis, complex carbohydrate degradation, amino acid synthesis and metabolism, purine and pyrimidine metabolism, isoprenoid biosynthesis, lipid metabolism, and co-factor biosynthesis were present in each of the healthy and caries groups. Our results suggested that the fundamental differences in dental plaque ecology partially explained the patients' susceptibility to caries, and could be used for caries risk prediction in the future.
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Affiliation(s)
- Jinzhi He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Hangzhou, Zhejiang, China
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Yichen Ge
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Bomiao Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyu Hu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuxia Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA.
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
- Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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18
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Huson DH, Steel M, El-Hadidi M, Mitra S, Peter S, Willmann M. A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples. J Biotechnol 2017; 250:45-50. [PMID: 27984120 DOI: 10.1016/j.jbiotec.2016.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/20/2016] [Accepted: 10/24/2016] [Indexed: 10/20/2022]
Abstract
One important question in microbiome analysis is how to assess the homogeneity of the microbial composition in a given environment, with respect to a given analysis method. Do different microbial samples taken from the same environment follow the same taxonomic distribution of organisms, or the same distribution of functions? Here we provide a non-parametric statistical "triangulation test" to address this type of question. The test requires that multiple replicates are available for each of the biological samples, and it is based on three-way computational comparisons of samples. To illustrate the application of the test, we collected three biological samples taken from different locations in one piece of human stool, each represented by three replicates, and analyzed them using MEGAN. (Despite its name, the triangulation test does not require that the number of biological samples or replicates be three.) The triangulation test rejects the null hypothesis that the three biological samples exhibit the same distribution of taxa or function (error probability ≤0.05), indicating that the microbial composition of the investigated human stool is not homogenous on a macroscopic scale, suggesting that pooling material from multiple locations is a reasonable practice. We provide an implementation of the test in our open source program MEGAN Community Edition.
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Affiliation(s)
- Daniel H Huson
- Center for Bioinformatics, University of Tübingen, Germany.
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | | | - Suparna Mitra
- Faculty of Medicine and Health - University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany; German Center for Infection Research (DZIF), Partner Site Tübingen, Germany
| | - Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany; German Center for Infection Research (DZIF), Partner Site Tübingen, Germany
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Veiga P, Torres AC, Aneiros F, Sousa-Pinto I, Troncoso JS, Rubal M. Consistent patterns of variation in macrobenthic assemblages and environmental variables over multiple spatial scales using taxonomic and functional approaches. Mar Environ Res 2016; 120:191-201. [PMID: 27591515 DOI: 10.1016/j.marenvres.2016.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
Spatial variability of environmental factors and macrobenthos, using species and functional groups, was examined over the same scales (100s of cm to >100 km) in intertidal sediments of two transitional water systems. The objectives were to test if functional groups were a good species surrogate and explore the relationship between environmental variables and macrobenthos. Environmental variables, diversity and the multivariate assemblage structure showed the highest variability at the scale of 10s of km. However, abundance was more variable at 10s of m. Consistent patterns were achieved using species and functional groups therefore, these may be a good species surrogate. Total carbon, salinity and silt/clay were the strongest correlated with macrobenthic assemblages. Results are valuable for design and interpretation of future monitoring programs including detection of anthropogenic disturbances in transitional systems and propose improvements in environmental variable sampling to refine the assessment of their relationship with biological data across spatial scales.
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Affiliation(s)
- Puri Veiga
- Laboratory of Coastal Biodiversity, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, P 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n 4150-181 Porto, Portugal; Estación de Bioloxía Mariña da Graña, Universidade de Santiago de Compostela, Casa do Hórreo, Rúa da Ribeira 1, 15590, A Graña, Ferrol, Spain.
| | - Ana Catarina Torres
- Laboratory of Coastal Biodiversity, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, P 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n 4150-181 Porto, Portugal
| | - Fernando Aneiros
- Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias do Mar, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; ECIMAT, Estación de Ciencias Mariñas de Toralla, Universidade de Vigo, Illa de Toralla, 36331 Vigo, Spain
| | - Isabel Sousa-Pinto
- Laboratory of Coastal Biodiversity, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, P 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n 4150-181 Porto, Portugal
| | - Jesús S Troncoso
- Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias do Mar, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; ECIMAT, Estación de Ciencias Mariñas de Toralla, Universidade de Vigo, Illa de Toralla, 36331 Vigo, Spain
| | - Marcos Rubal
- Laboratory of Coastal Biodiversity, Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Rua dos Bragas 289, P 4050-123 Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n 4150-181 Porto, Portugal; Departamento de Ecoloxía e Bioloxía Animal, Facultade de Ciencias do Mar, Universidade de Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
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