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Hong JK, Choi Y, Ahn S, Kim J, Yang DJ, Heo J, Cho JC, Lee TK. The impact of bioaerosol trajectories on microbial community assembly and physicochemical dynamics in the atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172736. [PMID: 38663612 DOI: 10.1016/j.scitotenv.2024.172736] [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: 01/29/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
This study explored the assembly mechanisms and physicochemical dynamics of microbial communities within atmospheric bioaerosols, focusing on the influence of different aerial trajectories. Over two years, samples near Seoul were classified into 'North', 'Southwest', and 'Others' categories based on their aerial trajectories. Physicochemical analysis of the PM2.5 particles revealed distinct ion compositions for each cluster, reflecting diverse environmental influences. Microbial community analysis revealed that shared dominant bacterial phyla were present in all clusters. However, distinct taxonomic profiles and biomarkers were also evident, such as coastal bacteria in the 'Southwest' cluster correlating with wind speed, and arid soil-originated bacteria in the 'North' cluster correlating with cations. These findings demonstrate that biomarkers in each cluster are representative of the distinct environments associated with their aerial trajectories. Notably, cluster 'Southwest' the highest microbial diversity and a strong alignment with the neutral community model, suggesting a large influence of passive dispersal from marine environments. Contrarily, 'North' and 'Others' were more influenced by niche-dependent factors. This study highlights the complex interplay between environmental factors and microbial dynamics in bioaerosols and provides important insights for environmental monitoring and public health risk assessment.
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Affiliation(s)
- Jin-Kyung Hong
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea
| | - Yongjoo Choi
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Seokhyun Ahn
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea
| | - Jeonghwan Kim
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Dong Jin Yang
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Jongwon Heo
- Gyeonggi-do Institute of Health & Environment, Suwon, Republic of Korea
| | - Jae-Chang Cho
- Department of Environmental Science, Hankuk University of Foreign Studies, Yongin, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea.
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2
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Han Y, Zhang M, Chen X, Zhai W, Tan E, Tang K. Transcriptomic evidences for microbial carbon and nitrogen cycles in the deoxygenated seawaters of Bohai Sea. ENVIRONMENT INTERNATIONAL 2022; 158:106889. [PMID: 34619534 DOI: 10.1016/j.envint.2021.106889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Eutrophication-induced water deoxygenation occurs continually in coastal oceans, and alters community structure, metabolic processes, and the energy shunt, resulting in a major threat to the ecological environment. Seasonal deoxygenation events have occurred in the Bohai Sea (China), however, how these affect the functional activity of microorganisms remains unclear. Here, through the use of absolute quantification of 16S rRNA genes amplicon sequencing and metatranscriptomics approaches, we investigated the structure of the microbial community and the patterns of transcriptional activity in deoxygenated seawaters. The dominant phyla were Proteobacteria (average value, 1.4 × 106 copies ml-1), Cyanobacteria (3.7 × 105 copies ml-1), Bacteroidetes (2.7 × 105 copies ml-1), and the ammonia-oxidizing archaea Thaumarchaeota (1.9 × 105 copies ml-1). Among the various environmental factors, dissolved oxygen, pH and temperature displayed the most significant correlation with microbial community composition and functional activity. Metatranscriptomic data showed high transcriptional activity of Thaumarchaeota in the deoxygenated waters, with a significant increase in the expression of core genes representing ammonia oxidation, ammonia transport, and carbon fixation (3-hydroxypropionic acid/4-hydroxybutyric acid cycle) pathways. The transcripts of Cyanobacteria involved in photosynthesis and carbon fixation (Calvin-Benson-Bassham cycle) significantly decreased in low oxygen waters. Meanwhile, the transcripts for the ribulose bisphosphate carboxylase-encoding gene shifted from being assigned to photoautotrophic to chemoautotrophic organisms in surface and bottom waters, respectively. Moreover, the transcription profile indicated that heterotrophs play a critical role in transforming low-molecular-weight dissolved organic nitrogen. Elevated abundances of transcripts related to microbial antioxidant activity corresponded to an enhanced aerobic metabolism of Thaumarchaeota in the low oxygen seawater. In general, our transcriptional evidences showed a population increase of Thaumarchaeota, especially the coastal ecotype of ammonia oxidizers, in low oxygen aquatic environments, and indicated an enhanced contribution of chemolithoautotrophic carbon fixation to carbon flow.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Weidong Zhai
- Institute of Marine Science and Technology, Shandong University, Qingdao 266000, Shandong, PR China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, Hainan, PR China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, PR China.
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3
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Baker KD, Kellogg CTE, McClelland JW, Dunton KH, Crump BC. The Genomic Capabilities of Microbial Communities Track Seasonal Variation in Environmental Conditions of Arctic Lagoons. Front Microbiol 2021; 12:601901. [PMID: 33643234 PMCID: PMC7906997 DOI: 10.3389/fmicb.2021.601901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
In contrast to temperate systems, Arctic lagoons that span the Alaska Beaufort Sea coast face extreme seasonality. Nine months of ice cover up to ∼1.7 m thick is followed by a spring thaw that introduces an enormous pulse of freshwater, nutrients, and organic matter into these lagoons over a relatively brief 2–3 week period. Prokaryotic communities link these subsidies to lagoon food webs through nutrient uptake, heterotrophic production, and other biogeochemical processes, but little is known about how the genomic capabilities of these communities respond to seasonal variability. Replicate water samples from two lagoons and one coastal site near Kaktovik, AK were collected in April (full ice cover), June (ice break up), and August (open water) to represent winter, spring, and summer, respectively. Samples were size fractionated to distinguish free-living and particle-attached microbial communities. Multivariate analysis of metagenomes indicated that seasonal variability in gene abundances was greater than variability between size fractions and sites, and that June differed significantly from the other months. Spring (June) gene abundances reflected the high input of watershed-sourced nutrients and organic matter via spring thaw, featuring indicator genes for denitrification possibly linked to greater organic carbon availability, and genes for processing phytoplankton-derived organic matter associated with spring blooms. Summer featured fewer indicator genes, but had increased abundances of anoxygenic photosynthesis genes, possibly associated with elevated light availability. Winter (April) gene abundances suggested low energy inputs and autotrophic bacterial metabolism, featuring indicator genes for chemoautotrophic carbon fixation, methane metabolism, and nitrification. Winter indicator genes for nitrification belonged to Thaumarchaeota and Nitrosomonadales, suggesting these organisms play an important role in oxidizing ammonium during the under-ice period. This study shows that high latitude estuarine microbial assemblages shift metabolic capabilities as they change phylogenetic composition between these extreme seasons, providing evidence that these communities may be resilient to large hydrological events in a rapidly changing Arctic.
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Affiliation(s)
- Kristina D Baker
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - James W McClelland
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Kenneth H Dunton
- The University of Texas at Austin Marine Science Institute, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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4
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Lai D, Hedlund BP, Xie W, Liu J, Phelps TJ, Zhang C, Wang P. Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments. Front Microbiol 2020; 11:572017. [PMID: 33224115 PMCID: PMC7674655 DOI: 10.3389/fmicb.2020.572017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C31. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C31 and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.
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Affiliation(s)
- Dengxun Lai
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China.,School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingjing Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Tommy J Phelps
- Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, Grosch R, Pühler A, Sczyrba A, Schlüter A. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes (Basel) 2019; 10:E424. [PMID: 31163637 PMCID: PMC6627896 DOI: 10.3390/genes10060424] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe-plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant-growth-promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.
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Affiliation(s)
- Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Timo Wentong Lin
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Wiebke Pätzold
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Sebastian Jaenicke
- Justus-Liebig-University Gießen, Bioinformatics & Systems Biology, Heinrich-Buff-Ring 58, 35392 Gießen, Germany.
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ) Großbeeren/Erfurt eV, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Computational Metagenomics Group, Universitätsstraße 27, 33615 Bielefeld, Germany.
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Genome Research of Industrial Microorganisms, Universitätsstraße 27, 33615 Bielefeld, Germany.
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6
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Kalwasińska A, Deja-Sikora E, Szabó A, Felföldi T, Kosobucki P, Brzezinska MS, Walczak M. Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:842-854. [PMID: 30481711 DOI: 10.1016/j.scitotenv.2018.11.246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3-25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.
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Affiliation(s)
- Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland.
| | - Edyta Deja-Sikora
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland; Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Attila Szabó
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, PázmányPéterstny. 1/c. H-1117 Budapest, Hungary
| | - Przemysław Kosobucki
- Department of Food Analysis and Environmental Protection, Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
| | - Maciej Walczak
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100 Toruń, Poland
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Araújo MB, Anderson RP, Márcia Barbosa A, Beale CM, Dormann CF, Early R, Garcia RA, Guisan A, Maiorano L, Naimi B, O’Hara RB, Zimmermann NE, Rahbek C. Standards for distribution models in biodiversity assessments. SCIENCE ADVANCES 2019; 5:eaat4858. [PMID: 30746437 PMCID: PMC6357756 DOI: 10.1126/sciadv.aat4858] [Citation(s) in RCA: 284] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
Demand for models in biodiversity assessments is rising, but which models are adequate for the task? We propose a set of best-practice standards and detailed guidelines enabling scoring of studies based on species distribution models for use in biodiversity assessments. We reviewed and scored 400 modeling studies over the past 20 years using the proposed standards and guidelines. We detected low model adequacy overall, but with a marked tendency of improvement over time in model building and, to a lesser degree, in biological data and model evaluation. We argue that implementation of agreed-upon standards for models in biodiversity assessments would promote transparency and repeatability, eventually leading to higher quality of the models and the inferences used in assessments. We encourage broad community participation toward the expansion and ongoing development of the proposed standards and guidelines.
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Affiliation(s)
- Miguel B. Araújo
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Rui Nabeiro Biodiversity Chair, University of Évora, 7000 Évora, Portugal
| | - Robert P. Anderson
- Department of Biology, City College of New York, New York, NY 10031, USA
- Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - A. Márcia Barbosa
- Rui Nabeiro Biodiversity Chair, University of Évora, 7000 Évora, Portugal
| | - Colin M. Beale
- Department of Biology, University of York, York YO19 5PR, UK
| | - Carsten F. Dormann
- Biometry and Environmental System Analysis, University of Freiburg, D-79106 Freiburg, Germany
| | - Regan Early
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Raquel A. Garcia
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Rui Nabeiro Biodiversity Chair, University of Évora, 7000 Évora, Portugal
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
- Centre for Statistics in Ecology, Environment and Conservation (SEEC), University of Cape Town, Private Bag, Rondebosch, 7701 Cape Town, South Africa
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Luigi Maiorano
- Department of Biology and Biotechnologies Charles Darwin, University of Rome La Sapienza, Rome, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Babak Naimi
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Robert B. O’Hara
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany
- Landscape Dynamics, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Niklaus E. Zimmermann
- Department of Mathematical Sciences and Centre for Biodiversity Dynamics, NTNU, 7491 Trondheim, Norway
- Environmental Systems Science, Swiss Federal Institute of Technology ETH, Zürich, Switzerland
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, UK
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8
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Tian L. Relationship between environmental factors and the spatial distribution of Spermophilus dauricus during 2000-2015 in China. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2018; 62:1781-1789. [PMID: 30019314 DOI: 10.1007/s00484-018-1580-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
The Spermophilus dauricus is a rodent species that feeds on the tender parts of plants and seeds. It is also a natural carrier of the hepatitis B virus and the main host of the plague bacillus Yersinia pestis threatening human health and the cultivated ecosystems. Based on ecological niche modeling (ENM) for the MaxEnt model and ArcGIS for the Spatial Analyst model, we quantified the potential risk zone and spatial pattern of the S. dauricus outbreak during 2000-2015. We analyze the temporal and spatial variation for different levels of risk zones. The results showed that the S. dauricus was primarily distributed in the North China with arid and semi-arid regions. The suitable habitat of S. dauricus includes an annual precipitation of 250-700 mm year-1, a temperature of - 3 to 14 °C, the normalized differential vegetation index (NDVI) of 0.05-0.65, and an elevation of < 3800 m. Although the NDVI and precipitation were significantly increasing, the potential risk zone did not expand. But, this result can not mean the S. dauricus outbreak had been controlled, and the substantial additional efforts in the form of observational and/or experimental investigations are needed to explore the relationships between environmental factors and the habitat of the S. dauricus, ideally by including the influences from land cover, vegetation characteristics, and artificial disturbances.
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Affiliation(s)
- Li Tian
- Qianyanzhou Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.
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9
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Hong JK, Jho EH, Choi HS, Kang G. Role of hemoglobin in hemoglobin-based remediation of the crude oil-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1174-1181. [PMID: 30857082 DOI: 10.1016/j.scitotenv.2018.01.243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/24/2018] [Accepted: 01/24/2018] [Indexed: 06/09/2023]
Abstract
This study investigated the changes in the indigenous microbial community structure with hemoglobin (Hb) application to determine the role of Hb in Hb-based remediation of crude oil-contaminated soil. The phylogenetic diversity of the bacterial community showed that the Hb addition selected surfactants-producing species, thereby, promoting TPH degradation. The significant increase in the CO2 generation, which can be related to the increase in the bacterial abundance inferred from the 16S rRNA gene copy number, supports the enhanced TPH degradation with Hb application. The similar residual TPH concentrations in the presence of only hydrogen peroxide (H2O2) and both Hb and H2O2 suggested that the role of Hb as a catalyst was not as significant as the role of Hb as a nutrient. Also, in the presence of H2O2, a greater recovery of the microbial community structure was observed with the double Hb injection than the single Hb injection. Overall, this study shows that the Hb-based remediation strategies via microbial metabolism can be successfully applied to remediate the crude-oil contaminated Kuwaiti soil.
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Affiliation(s)
- Jin-Kyung Hong
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon-myeon, Cheoin-gu, Youngin-si, Gyeonggi-do 17035, Republic of Korea
| | - Eun Hea Jho
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon-myeon, Cheoin-gu, Youngin-si, Gyeonggi-do 17035, Republic of Korea.
| | - Hyo Sub Choi
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon-myeon, Cheoin-gu, Youngin-si, Gyeonggi-do 17035, Republic of Korea
| | - Guyoung Kang
- Department of Environmental Science, Hankuk University of Foreign Studies, 81 Oedae-ro, Mohyeon-myeon, Cheoin-gu, Youngin-si, Gyeonggi-do 17035, Republic of Korea
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Dat TTH, Steinert G, Thi Kim Cuc N, Smidt H, Sipkema D. Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam. PeerJ 2018; 6:e4970. [PMID: 29900079 PMCID: PMC5995103 DOI: 10.7717/peerj.4970] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Ha Noi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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Müller O, Wilson B, Paulsen ML, Rumińska A, Armo HR, Bratbak G, Øvreås L. Spatiotemporal Dynamics of Ammonia-Oxidizing Thaumarchaeota in Distinct Arctic Water Masses. Front Microbiol 2018; 9:24. [PMID: 29410658 PMCID: PMC5787140 DOI: 10.3389/fmicb.2018.00024] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/08/2018] [Indexed: 12/01/2022] Open
Abstract
One of the most abundant archaeal groups on Earth is the Thaumarchaeota. They are recognized as major contributors to marine ammonia oxidation, a crucial step in the biogeochemical cycling of nitrogen. Their universal success is attributed to a high genomic flexibility and niche adaptability. Based on differences in the gene coding for ammonia monooxygenase subunit A (amoA), two different ecotypes with distinct distribution patterns in the water column have been identified. We used high-throughput sequencing of 16S rRNA genes combined with archaeal amoA functional gene clone libraries to investigate which environmental factors are driving the distribution of Thaumarchaeota ecotypes in the Atlantic gateway to the Arctic Ocean through an annual cycle in 2014. We observed the characteristic vertical pattern of Thaumarchaeota abundance with high values in the mesopelagic (>200 m) water throughout the entire year, but also in the epipelagic (<200 m) water during the dark winter months (January, March and November). The Thaumarchaeota community was dominated by three OTUs which on average comprised 76% ± 11 and varied in relative abundance according to water mass characteristics and not to depth or ammonium concentration, as suggested in previous studies. The ratios of the abundance of the different OTU types were similar to that of the functional amoA water cluster types. Together, this suggests a strong selection of ecotypes within different water masses, supporting the general idea of water mass characteristics as an important factor in defining microbial community structure. If indeed, as suggested in this study, Thaumarchaeota population dynamics are controlled by a set of factors, described here as water mass characteristics and not just depth alone, then changes in water mass flow will inevitably affect the distribution of the different ecotypes.
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Affiliation(s)
- Oliver Müller
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Bryan Wilson
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Maria L Paulsen
- Department of Microbiology, University of Bergen, Bergen, Norway
| | | | - Hilde R Armo
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Gunnar Bratbak
- Department of Microbiology, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Microbiology, University of Bergen, Bergen, Norway.,University Center in Svalbard (UNIS), Longyearbyen, Norway
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Sebastián M, Auguet JC, Restrepo-Ortiz CX, Sala MM, Marrasé C, Gasol JM. Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation. Environ Microbiol 2017; 20:713-723. [PMID: 29159926 DOI: 10.1111/1462-2920.14002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/17/2017] [Indexed: 11/28/2022]
Abstract
The bathypelagic ocean is one of the largest ecosystems on Earth and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilization of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 year) dynamics of an enclosed community. Despite the lack of external energy supply, we observed a continuous succession of active prokaryotic phylotypes, which was driven by recruitment of taxa from the seed bank (i.e., initially rare operational taxonomic units [OTUs]). A single OTU belonging to Marine Group I of Thaumarchaeota, which was originally rare, dominated the microbial community for ∼ 4 months and played a fundamental role in this succession likely by introducing new organic carbon through chemolithoautotrophy. This carbon presumably produced a priming effect, because after the decline of Thaumarchaeota, the diversity and metabolic potential of the community increased back to the levels present at the start of the experiment. Our study demonstrates the profound versatility of deep microbial communities when facing organic carbon deprivation.
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Affiliation(s)
- Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, Passeig Marítim de la Barceloneta, 37-49, E08003 Barcelona, Catalunya, Spain.,Instituto de Oceanografía y Cambio Global, Universidad de Las Palmas de Gran Canaria, Parque Científico Tecnológico Marino de Taliarte, s/n 35214, Telde, Spain
| | - Jean-Christophe Auguet
- Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR CNRS 9190, Université de Montpellier, CC093, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Claudia Ximena Restrepo-Ortiz
- Marine Biodiversity, Exploitation and Conservation (MARBEC), UMR CNRS 9190, Université de Montpellier, CC093, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - María Montserrat Sala
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, Passeig Marítim de la Barceloneta, 37-49, E08003 Barcelona, Catalunya, Spain
| | - Celia Marrasé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, Passeig Marítim de la Barceloneta, 37-49, E08003 Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, Passeig Marítim de la Barceloneta, 37-49, E08003 Barcelona, Catalunya, Spain
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Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:3762159. [PMID: 27006640 PMCID: PMC4783532 DOI: 10.1155/2016/3762159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/14/2015] [Accepted: 01/10/2016] [Indexed: 12/28/2022]
Abstract
This study compared soil archaeal communities of the Amazon forest with that of an adjacent area under oil palm cultivation by 16S ribosomal RNA gene pyrosequencing. Species richness and diversity were greater in native forest soil than in the oil palm-cultivated area, and 130 OTUs (13.7%) were shared between these areas. Among the classified sequences, Thaumarchaeota were predominant in the native forest, whereas Euryarchaeota were predominant in the oil palm-cultivated area. Archaeal species diversity was 1.7 times higher in the native forest soil, according to the Simpson diversity index, and the Chao1 index showed that richness was five times higher in the native forest soil. A phylogenetic tree of unclassified Thaumarchaeota sequences showed that most of the OTUs belong to Miscellaneous Crenarchaeotic Group. Several archaeal genera involved in nutrient cycling (e.g., methanogens and ammonia oxidizers) were identified in both areas, but significant differences were found in the relative abundances of Candidatus Nitrososphaera and unclassified Soil Crenarchaeotic Group (prevalent in the native forest) and Candidatus Nitrosotalea and unclassified Terrestrial Group (prevalent in the oil palm-cultivated area). More studies are needed to culture some of these Archaea in the laboratory so that their metabolism and physiology can be studied.
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