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Xia J, Yu K, Yao Z, Sheng H, Mao L, Lu D, Gan H, Zhang S, Zhu DZ. Toward an intensive understanding of sewer sediment prokaryotic community assembly and function. Front Microbiol 2023; 14:1327523. [PMID: 38173681 PMCID: PMC10761402 DOI: 10.3389/fmicb.2023.1327523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Prokaryotic communities play important roles in sewer sediment ecosystems, but the community composition, functional potential, and assembly mechanisms of sewer sediment prokaryotic communities are still poorly understood. Here, we studied the sediment prokaryotic communities in different urban functional areas (multifunctional, commercial, and residential areas) through 16S rRNA gene amplicon sequencing. Our results suggested that the compositions of prokaryotic communities varied significantly among functional areas. Desulfomicrobium, Desulfovibrio, and Desulfobacter involved in the sulfur cycle and some hydrolytic fermentation bacteria were enriched in multifunctional area, while Methanospirillum and Methanoregulaceae, which were related to methane metabolism were significantly discriminant taxa in the commercial area. Physicochemical properties were closely related to overall community changes (p < 0.001), especially the nutrient levels of sediments (i.e., total nitrogen and total phosphorus) and sediment pH. Network analysis revealed that the prokaryotic community network of the residential area sediment was more complex than the other functional areas, suggesting higher stability of the prokaryotic community in the residential area. Stochastic processes dominated the construction of the prokaryotic community. These results expand our understanding of the characteristics of prokaryotic communities in sewer sediment, providing a new perspective for studying sewer sediment prokaryotic community structure.
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Affiliation(s)
- Jingjing Xia
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Kai Yu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Zhiyuan Yao
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Huafeng Sheng
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lijuan Mao
- Zhenhai Urban Planning and Survey Research Institute of Ningbo, Ningbo, China
| | - Dingnan Lu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - HuiHui Gan
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
| | - Shulin Zhang
- Zhenhai Urban Planning and Survey Research Institute of Ningbo, Ningbo, China
| | - David Z. Zhu
- School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China
- Institute of Ocean Engineering, Ningbo University, Ningbo, China
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB, Canada
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Chen L, Xin X, Li J, Han C, Xiong W, Luo Y, Sun R, Zhang J. Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists. MICROBIAL ECOLOGY 2023; 86:2541-2551. [PMID: 37401933 DOI: 10.1007/s00248-023-02258-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with 13C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased 13C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and 13C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial 13C assimilation (i.e., 13C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.
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Affiliation(s)
- Lin Chen
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
| | - Xiuli Xin
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
| | - Jingwang Li
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changdong Han
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Ruibo Sun
- Anhui Province Key Laboratory of Farmland Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Jiabao Zhang
- Fengqiu Experimental Station of National Ecosystem Research Network of China, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, 210008, Jiangsu Province, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China.
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Dos Santos VL, Silva UC, Santos EH, Resende AA, Dias MF, Cuadros-Orellana S, Marques AR. Exploring the mycobiota of bromeliads phytotelmata in Brazilian Campos Rupestres. Braz J Microbiol 2023; 54:1885-1897. [PMID: 37322328 PMCID: PMC10485200 DOI: 10.1007/s42770-023-00977-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/10/2023] [Indexed: 06/17/2023] Open
Abstract
The phytotelmata is a water-filled tank on a terrestrial plant, and it plays an important role in bromeliad growth and ecosystem functioning. Even though previous studies have contributed to elucidate the composition of the prokaryotic component of this aquatic ecosystem, its mycobiota (fungal community) is still poorly known. In the present work, ITS2 amplicon deep sequencing was used to examine the fungal communities inhabiting the phytotelmata of two bromeliads species that coexist in a sun-exposed rupestrian field of Southeastern Brazil, namely Aechmea nudicaulis (AN) and Vriesea minarum (VM). Ascomycota was the most abundant phylum in both bromeliads (57.1 and 89.1% in AN and VM respectively, on average), while the others were present in low abundance (< 2%). Mortierellomycota and Glomeromycota were exclusively observed in AN. Beta-diversity analysis showed that samples from each bromeliad significantly clustered together. In conclusion, despite the considerable within-group variation, the results suggested that each bromeliad harbor a distinct fungi community, what could be associated with the physicochemical characteristics of the phytotelmata (mainly total nitrogen, total organic carbon, and total carbon) and plant morphological features.
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Affiliation(s)
- Vera Lúcia Dos Santos
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
| | - Ubiana Cássia Silva
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Eduardo Horta Santos
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Alessandra Abrão Resende
- Expertise Center Botany and Biodiversity, Museu de História Natural e Jardim Botânico, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31080-010, Brazil
| | - Marcela França Dias
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Sara Cuadros-Orellana
- Universidad Católica del Maule, Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales, 3480112, Talca, Chile
| | - Andréa Rodrigues Marques
- Department of Biological Sciences, Centro Federal de Educação Tecnológica de Minas Gerais - CEFET/MG, Av. Amazonas, 5253, Nova Suíça, 30.421-169, Belo Horizonte, MG, 30421-169, Brazil
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Metz HC, Miller AK, You J, Akorli J, Avila FW, Buckner EA, Kane P, Otoo S, Ponlawat A, Triana-Chávez O, Williams KF, McBride CS. Evolution of a Mosquito's Hatching Behavior to Match Its Human-Provided Habitat. Am Nat 2023; 201:200-214. [PMID: 36724468 DOI: 10.1086/722481] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractA subspecies of the yellow fever mosquito, Aedes aegypti, has recently evolved to specialize in biting and living alongside humans. It prefers human odor over the odor of nonhuman animals and breeds in human-provided artificial containers rather than the forest tree holes of its ancestors. Here, we report one way this human specialist has adapted to the distinct ecology of human environments. While eggs of the ancestral subspecies rarely hatch in pure water, those of the derived human specialist do so readily. We trace this novel behavior to a shift in how eggs respond to dissolved oxygen, low levels of which may signal food abundance. Moreover, we show that while tree holes are consistently low in dissolved oxygen, artificial containers often have much higher levels. There is thus a concordance between the hatching behavior of each subspecies and the aquatic habitat it uses in the wild. We find this behavioral variation is heritable, with both maternal and zygotic effects. The zygotic effect depends on dissolved oxygen concentration (i.e., a genotype-environment interaction, or G×E), pointing to potential changes in oxygen-sensitive circuits. Together, our results suggest that a shift in hatching response contributed to the pernicious success of this human-specialist mosquito and illustrate how animals may rapidly adapt to human-driven changes in the environment.
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North GB, Brinton EK, Kho TL, Fukui K, Maharaj FDR, Fung A, Ranganath M, Shiina JH. Acid waters in tank bromeliads: Causes and potential consequences. AMERICAN JOURNAL OF BOTANY 2023; 110:e16104. [PMID: 36571428 PMCID: PMC10107723 DOI: 10.1002/ajb2.16104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
PREMISE The consequences of acidity for plant performance are profound, yet the prevalence and causes of low pH in bromeliad tank water are unknown despite its functional relevance to key members of many neotropical plant communities. METHODS We investigated tank water pH for eight bromeliad species in the field and for the widely occurring Guzmania monostachia in varying light. We compared pH changes over time between plant and artificial tanks containing a solution combined from several plants. Aquaporin transcripts were measured for field plants at two levels of pH. We investigated relationships between pH, leaf hydraulic conductance, and CO2 concentration in greenhouse plants and tested proton pump activity using a stimulator and inhibitor. RESULTS Mean tank water pH for the eight species was 4.7 ± 0.06 and was lower for G. monostachia in higher light. The pH of the solution in artificial tanks, unlike in plants, did not decrease over time. Aquaporin transcription was higher for plants with lower pH, but leaf hydraulic conductance did not differ, suggesting that the pH did not influence water uptake. Tank pH and CO2 concentration were inversely related. Fusicoccin enhanced a decrease in tank pH, whereas orthovanadate did not. CONCLUSIONS Guzmania monostachia acidified its tank water via leaf proton pumps, which appeared responsive to light. Low pH increased aquaporin transcripts but did not influence leaf hydraulic conductance, hence may be more relevant to nutrient uptake.
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Affiliation(s)
| | - Erin K. Brinton
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
| | - Tiffany L. Kho
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
| | - Kyle Fukui
- Department of BiochemistryOccidental CollegeLos AngelesCA90041USA
| | | | - Adriana Fung
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
| | - Mira Ranganath
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
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Aguilar-Cruz Y, Milke F, Leinberger J, Poehlein A, Zotz G, Brinkhoff T. Diversity and putative metabolic function of prokaryotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Front Microbiol 2022; 13:945488. [PMID: 36312956 PMCID: PMC9608151 DOI: 10.3389/fmicb.2022.945488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
Tank bromeliads are unique canopy microhabitats that offer freshwater and organic nutrient-rich substrates in the Neotropics. In them it is possible to thoroughly characterize environmental factors and species composition of terrestrial and aquatic biota. Therefore, these plants have been used as natural models to study how communities are distributed and assembled. Here we used amplicon sequencing of the 16S rRNA gene and their functional annotations to study the diversity and metabolic potential of prokaryotic communities in tank bromeliads in five different forests along an elevation gradient in tropical Mexico. Furthermore, we analyzed the effects of vegetation type and environmental factors inside the tanks on prokaryotic composition. We found a high prokaryotic diversity in tank bromeliads along the elevation gradient. Prokaryotes commonly observed in acidic environments rich in organic carbon, and the potential pathogen Pasteurella multocida, were present in all samples, but few amplicon sequence variants were shared between forests. The prokaryotic composition was affected by forest type, and comparisons against null models suggest that it was shaped by non-neutral processes. Furthermore, prokaryotic community changes significantly covaried with tank water temperature, pH, and inorganic carbon. We found a high diversity of putative metabolic groups dominated by chemoheterotrophs and fermenters, but taxonomic groups involved in nitrogen and sulfur cycling were also present in all samples. These results suggest that tank bromeliads promote taxonomic and metabolic diversity of the prokaryotic community at a local and regional scale and play an important role in the biogeochemistry of forest canopies in the Neotropics.
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Affiliation(s)
- Yonatan Aguilar-Cruz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Felix Milke
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- *Correspondence: Yonatan Aguilar-Cruz, ; Felix Milke,
| | - Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Gerhard Zotz
- Functional Ecology of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Bacterial Communities of Forest Soils along Different Elevations: Diversity, Structure, and Functional Composition with Potential Impacts on CO 2 Emission. Microorganisms 2022; 10:microorganisms10040766. [PMID: 35456816 PMCID: PMC9032212 DOI: 10.3390/microorganisms10040766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
Soil bacteria are important components of forest ecosystems, there compostion structure and functions are sensitive to environmental conditions along elevation gradients. Using 16S rRNA gene amplicon sequencing followed by FAPROTAX function prediction, we examined the diversity, composition, and functional potentials of soil bacterial communities at three sites at elevations of 1400 m, 1600 m, and 2200 m in a temperate forest. We showed that microbial taxonomic composition did not change with elevation (p = 0.311), though soil bacterial α-diversities did. Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia were abundant phyla in almost all soil samples, while Nitrospirae, closely associated with soil nitrogen cycling, was the fourth most abundant phylum in soils at 2200 m. Chemoheterotrophy and aerobic chemoheterotrophy were the two most abundant functions performed in soils at 1400 m and 1600 m, while nitrification (25.59% on average) and aerobic nitrite oxidation (19.38% on average) were higher in soils at 2200 m. Soil CO2 effluxes decreased (p < 0.050) with increasing elevation, while they were positively correlated (r = 0.55, p = 0.035) with the abundances of bacterial functional groups associated with carbon degradation. Moreover, bacterial functional composition, rather than taxonomic composition, was significantly associated with soil CO2 effluxes, suggesting a decoupling of taxonomy and function, with the latter being a better predictor of ecosystem functions. Annual temperature, annual precipitation, and pH shaped (p < 0.050) both bacterial taxonomic and functional communities. By establishing linkages between bacterial taxonomic communities, abundances of bacterial functional groups, and soil CO2 fluxes, we provide novel insights into how soil bacterial communities could serve as potential proxies of ecosystem functions.
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Muneer MA, Hou W, Li J, Huang X, Ur Rehman Kayani M, Cai Y, Yang W, Wu L, Ji B, Zheng C. Soil pH: a key edaphic factor regulating distribution and functions of bacterial community along vertical soil profiles in red soil of pomelo orchard. BMC Microbiol 2022; 22:38. [PMID: 35109809 PMCID: PMC8808772 DOI: 10.1186/s12866-022-02452-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Soil microbes exist throughout the soil profile and those inhabiting topsoil (0–20 cm) are believed to play a key role in nutrients cycling. However, the majority of the soil microbiology studies have exclusively focused on the distribution of soil microbial communities in the topsoil, and it remains poorly understood through the subsurface soil profile (i.e., 20–40 and 40–60 cm). Here, we examined how the bacterial community composition and functional diversity changes under intensive fertilization across vertical soil profiles [(0–20 cm (RS1), 20–40 cm (RS2), and 40–60 cm (RS3)] in the red soil of pomelo orchard, Pinghe County, Fujian, China. Results Bacterial community composition was determined by 16S rRNA gene sequencing and interlinked with edaphic factors, including soil pH, available phosphorous (AP), available nitrogen (AN), and available potassium (AK) to investigate the key edaphic factors that shape the soil bacterial community along with different soil profiles. The most dominant bacterial taxa were Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Crenarchaeota, and Bacteriodetes. Bacterial richness and diversity was highest in RS1 and declined with increasing soil depth. The distinct distribution patterns of the bacterial community were found across the different soil profiles. Besides, soil pH exhibited a strong influence (pH ˃AP ˃AN) on the bacterial communities under all soil depths. The relative abundance of Proteobacteria, Actinobacteria, Crenarchaeota, and Firmicutes was negatively correlated with soil pH, while Acidobacteria, Chloroflexi, Bacteriodetes, Planctomycetes, and Gemmatimonadetes were positively correlated with soil pH. Co-occurrence network analysis revealed that network topological features were weakened with increasing soil depth, indicating a more stable bacterial community in the RS1. Bacterial functions were estimated using FAPROTAX and the relative abundance of functional bacterial community related to metabolic processes, including C-cycle, N-cycle, and energy production was significantly higher in RS1 compared to RS2 and RS3, and soil pH had a significant effect on these functional microbes. Conclusions This study provided the valuable findings regarding the structure and functions of bacterial communities in red soil of pomelo orchards, and highlighted the importance of soil depth and pH in shaping the soil bacterial population, their spatial distribution and ecological functioning. These results suggest the alleviation of soil acidification by adopting integrated management practices to preserve the soil microbial communities for better ecological functioning. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02452-x.
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Affiliation(s)
- Muhammad Atif Muneer
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Hou
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jian Li
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoman Huang
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Masood Ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, School of Medicine, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuanyang Cai
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenhao Yang
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangquan Wu
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baoming Ji
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Chaoyuan Zheng
- College of Resources and Environment, International Magnesium Institute, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Huang L, Luo J, Li L, Jiang H, Sun X, Yang J, She W, Liu W, Li L, Davis AP. Unconventional microbial mechanisms for the key factors influencing inorganic nitrogen removal in stormwater bioretention columns. WATER RESEARCH 2022; 209:117895. [PMID: 34864344 DOI: 10.1016/j.watres.2021.117895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Bioretention systems are environmentally friendly measures to control the amount of water and pollutants in urban stormwater runoff, and their treatment performance for inorganic N strongly depends on various microbial processes. However, microbial responses to variations of N mass reduction in bioretention systems are complex and poorly understood, which is not conducive to management designs. In the present study, a series of bioretention columns were established to monitor their fate performance for inorganic N (NH4+and NO3-) by using different configurations and by dosing with simulated stormwater events. The results showed that NH4+ was efficiently oxidized to NO3-, mainly by ammonia- and nitrite-oxidizing bacteria in the oxic media, regardless of the configurations of the bioretention systems or stormwater conditions. In contrast, NO3- removal pathways varied greatly in different columns. The presence of vegetation efficiently improved NO3-mass reduction through root assimilation and enhancement of microbial NO3- reduction in the rhizosphere. The construction of an organic-rich saturation zone can make the redox potential too low for heterotrophic denitrification to occur, so as to ensure high NO3- mass reduction mainly via stimulating chemolithotrophic NO3- reduction coupled with oxidation of reductive sulfur compounds derived from the bio-reduction of sulfate. In contrast, in the organic-poor saturation zone, multiple oligotrophic NO3- reduction pathways may be responsible for the high NO3- mass reduction. These findings highlight the necessity of considering the variation of N bio-transformation pathways for inorganic N removal in the configuration of bioretention systems.
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Affiliation(s)
- Liuqin Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China
| | - Junyue Luo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Linxin Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Wen Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Liqing Li
- School of Environmental Science, China University of Geosciences, Wuhan 430074, China.
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20742, USA
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10
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Herrera-García JA, Martinez M, Zamora-Tavares P, Vargas-Ponce O, Hernández-Sandoval L, Rodríguez-Zaragoza FA. Metabarcoding of the phytotelmata of Pseudalcantarea grandis (Bromeliaceae) from an arid zone. PeerJ 2022; 10:e12706. [PMID: 35127281 PMCID: PMC8801176 DOI: 10.7717/peerj.12706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 12/07/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Pseudalcantarea grandis (Schltdl.) Pinzón & Barfuss is a tank bromeliad that grows on cliffs in the southernmost portion of the Chihuahuan desert. Phytotelmata are water bodies formed by plants that function as micro-ecosystems where bacteria, algae, protists, insects, fungi, and some vertebrates can develop. We hypothesized that the bacterial diversity contained in the phytotelma formed in a bromeliad from an arid zone would differ in sites with and without surrounding vegetation. Our study aimed to characterize the bacterial composition and putative metabolic functions in P. grandis phytotelmata collected in vegetated and non-vegetated sites. METHODS Water from 10 individuals was sampled. Five individuals had abundant surrounding vegetation, and five had little or no vegetation. We extracted DNA and amplified seven hypervariable regions of the 16S gene (V2, V4, V8, V3-6, 7-9). Metabarcoding sequencing was performed on the Ion Torrent PGM platform. Taxonomic identity was assigned by the binning reads and coverage between hit and query from the reference database of at least 90%. Putative metabolic functions of the bacterial families were assigned mainly using the FAPROTAX database. The dominance patterns in each site were visualized with rank/abundance curves using the number of Operational Taxonomic Units (OTUs) per family. A percentage similarity analysis (SIMPER) was used to estimate dissimilarity between the sites. Relationships among bacterial families (identified by the dominance analysis and SIMPER), sites, and their respective putative functions were analyzed with shade plots. RESULTS A total of 1.5 million useful bacterial sequences were obtained. Sequences were clustered into OTUs, and taxonomic assignment was conducted using BLAST in the Greengenes databases. Bacterial diversity was 23 phyla, 52 classes, 98 orders, 218 families, and 297 genera. Proteobacteria (37%), Actinobacteria (19%), and Firmicutes (15%) comprised the highest percentage (71%). There was a 68.3% similarity between the two sites at family level, with 149 families shared. Aerobic chemoheterotrophy and fermentation were the main metabolic functions in both sites, followed by ureolysis, nitrate reduction, aromatic compound degradation, and nitrogen fixation. The dominant bacteria shared most of the metabolic functions between sites. Some functions were recorded for one site only and were related to families with the lowest OTUs richness. Bacterial diversity in the P. grandis tanks included dominant phyla and families present at low percentage that could be considered part of a rare biosphere. A rare biosphere can form genetic reservoirs, the local abundance of which depends on external abiotic and biotic factors, while their interactions could favor micro-ecosystem resilience and resistance.
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Affiliation(s)
| | - Mahinda Martinez
- Universidad Autónoma de Querétaro, Querétaro, Mexico,Laboratorio Nacional de Identificación y Caracterización Vegetal, Querétaro, Mexico
| | - Pilar Zamora-Tavares
- Instituto de Botánica, departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México,Laboratorio Nacional de Identificación y Caracterización Vegetal, Guadalajara, Mexico
| | - Ofelia Vargas-Ponce
- Instituto de Botánica, departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, México,Laboratorio Nacional de Identificación y Caracterización Vegetal, Guadalajara, Mexico
| | - Luis Hernández-Sandoval
- Universidad Autónoma de Querétaro, Querétaro, Mexico,Laboratorio Nacional de Identificación y Caracterización Vegetal, Querétaro, Mexico
| | - Fabián Alejandro Rodríguez-Zaragoza
- Laboratorio de Ecología Molecular, Microbiología y Taxonomía (LEMITAX), Departamento de Ecología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
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11
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [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: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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12
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Deng S, Wang B, Zhang W, Su S, Dong H, Banat IM, Sun S, Guo J, Liu W, Wang L, She Y, Zhang F. Elucidate microbial characteristics in a full-scale treatment plant for offshore oil produced wastewater. PLoS One 2021; 16:e0255836. [PMID: 34383807 PMCID: PMC8360554 DOI: 10.1371/journal.pone.0255836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/24/2021] [Indexed: 11/19/2022] Open
Abstract
Oil-produced wastewater treatment plants, especially those involving biological treatment processes, harbor rich and diverse microbes. However, knowledge of microbial ecology and microbial interactions determining the efficiency of plants for oil-produced wastewater is limited. Here, we performed 16S rDNA amplicon sequencing to elucidate the microbial composition and potential microbial functions in a full-scale well-worked offshore oil-produced wastewater treatment plant. Results showed that microbes that inhabited the plant were diverse and originated from oil and marine associated environments. The upstream physical and chemical treatments resulted in low microbial diversity. Organic pollutants were digested in the anaerobic baffled reactor (ABR) dominantly through fermentation combined with sulfur compounds respiration. Three aerobic parallel reactors (APRs) harbored different microbial groups that performed similar potential functions, such as hydrocarbon degradation, acidogenesis, photosynthetic assimilation, and nitrogen removal. Microbial characteristics were important to the performance of oil-produced wastewater treatment plants with biological processes.
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Affiliation(s)
- Shuyuan Deng
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Bo Wang
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Wenda Zhang
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Sanbao Su
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Hao Dong
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Ibrahim M. Banat
- Faculty of Life and Health Sciences, University of Ulster, Coleraine, N. Ireland, United Kingdom
| | - Shanshan Sun
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Jianping Guo
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
| | - Weiming Liu
- Sinopec Shengli Oilfield, Dongying, Shangdong, China
| | - Linhai Wang
- CNOOC Energy Development Co. Ltd. Technology Branch, Beijing, China
| | - Yuehui She
- College of Petroleum Engineering, Yangtze University, Wuhan, Hubei, China
| | - Fan Zhang
- School of Energy Resources, China University of Geosciences (Beijing), Beijing, China
- * E-mail:
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13
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Gralka M, Szabo R, Stocker R, Cordero OX. Trophic Interactions and the Drivers of Microbial Community Assembly. Curr Biol 2021; 30:R1176-R1188. [PMID: 33022263 DOI: 10.1016/j.cub.2020.08.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function. Here, we review experimental and theoretical advances to argue that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly. Trophic interactions emerge from the deconstruction of complex forms of organic matter into a wealth of smaller metabolic intermediates, some of which are released to the environment and serve as a nutritional buffet for the community. The structure of the emergent trophic network and the rate at which primary resources are supplied control many features of microbial community assembly, including the relative contributions of competition and cooperation and the emergence of alternative community states. Viewing microbial community assembly through the lens of trophic interactions also has important implications for the spatial dynamics of communities as well as the functional redundancy of taxonomic groups. Given the ubiquity of trophic interactions across environments, they impart a common logic that can enable the development of a more quantitative and predictive microbial community ecology.
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Affiliation(s)
- Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel Szabo
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich 8093, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Bergelson J, Kreitman M, Petrov DA, Sanchez A, Tikhonov M. Functional biology in its natural context: A search for emergent simplicity. eLife 2021; 10:e67646. [PMID: 34096867 PMCID: PMC8184206 DOI: 10.7554/elife.67646] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/28/2021] [Indexed: 01/03/2023] Open
Abstract
The immeasurable complexity at every level of biological organization creates a daunting task for understanding biological function. Here, we highlight the risks of stripping it away at the outset and discuss a possible path toward arriving at emergent simplicity of understanding while still embracing the ever-changing complexity of biotic interactions that we see in nature.
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Affiliation(s)
- Joy Bergelson
- Department of Ecology & Evolution, University of ChicagoChicagoUnited States
| | - Martin Kreitman
- Department of Ecology & Evolution, University of ChicagoChicagoUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale UniversityNew HavenUnited States
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St LouisSt. LouisUnited States
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15
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Almeida AM, Souza RM. Nematode trophic structure in the phytotelma of Neoregelia cruenta (Bromeliaceae) in relation to microenvironmental and climate variables. J Nematol 2021; 52:e2020-100. [PMID: 33829205 PMCID: PMC8015368 DOI: 10.21307/jofnem-2020-100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Indexed: 11/22/2022] Open
Abstract
The term phytotelma (pl. phytotelmata) designates a plant-associated reservoir of fresh water and organic debris. Phytotelmata in tank bromeliads are abundant in tropical forests, and they provide shelter, food, and water for many metazoans. Among the invertebrates known to inhabit phytotelmata, nematodes are the least studied, despite their important role in nutrient and energy cycles in freshwater ecosystems. This study was conceived to characterize the nematode trophic structure in the phytotelma of the bromeliad N. cruenta, and to identify climate and microenvironmental variables that impact it. Nematode abundance (total and per trophic group), rainfall, air temperature, the amount of organic debris fallen into the phytotelma, and eight physico-chemical properties (PCPs) of the water retained in the bromeliad tank – volume; temperature; pH; dissolved organic carbon, nitrogen, oxygen, and solids; and electrical conductivity – were monitored during two years in a natural reserve in Brazil. Bacterial and hyphal feeder nematodes predominated over other trophic groups. Nematode abundance (total and per trophic group) was not impacted by fluctuations in rainfall or air temperature. The amount of organic debris fallen into the phytotelma correlated positively with nematode abundance (total and per trophic group). Regarding the PCPs of water, the only significant correlation – positive – was between the amount of dissolved oxygen and the abundance of hyphal feeder nematodes. These results bring a clearer understanding of the ecology of nematodes inhabiting phytotelmata, which are peculiar and understudied freshwater ecosystems.
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Affiliation(s)
- Alexandre M Almeida
- Nematology Research Group, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ricardo M Souza
- Nematology Research Group, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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16
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Bao Y, Dolfing J, Guo Z, Chen R, Wu M, Li Z, Lin X, Feng Y. Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils. MICROBIOME 2021; 9:84. [PMID: 33827695 PMCID: PMC8028251 DOI: 10.1186/s40168-021-01032-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbial-driven decomposition of plant residues is integral to carbon sequestration in terrestrial ecosystems. Actinobacteria, one of the most widely distributed bacterial phyla in soils, are known for their ability to degrade plant residues in vitro. However, their in situ importance and specific activity across contrasting ecological environments are not known. Here, we conducted three field experiments with buried straw in combination with microcosm experiments with 13C-straw in paddy soils under different soil fertility levels to reveal the ecophysiological roles of Actinobacteria in plant residue decomposition. RESULTS While accounting for only 4.6% of the total bacterial abundance, the Actinobacteria encoded 16% of total abundance of carbohydrate-active enzymes (CAZymes). The taxonomic and functional compositions of the Actinobacteria were, surprisingly, relatively stable during straw decomposition. Slopes of linear regression models between straw chemical composition and Actinobacterial traits were flatter than those for other taxonomic groups at both local and regional scales due to holding genes encoding for full set of CAZymes, nitrogenases, and antibiotic synthetases. Ecological co-occurrence network and 13C-based metagenomic analyses both indicated that their importance for straw degradation increased in less fertile soils, as both links between Actinobacteria and other community members and relative abundances of their functional genes increased with decreasing soil fertility. CONCLUSIONS This study provided DNA-based evidence that non-dominant Actinobacteria plays a key ecophysiological role in plant residue decomposition as their members possess high proportions of CAZymes and as a group maintain a relatively stable presence during plant residue decomposition both in terms of taxonomic composition and functional roles. Their importance for decomposition was more pronounced in less fertile soils where their possession functional genes and interspecies interactions stood out more. Our work provides new ecophysiological angles for the understanding of the importance of Actinobacteria in global carbon cycling. Video abstract.
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Affiliation(s)
- Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Jan Dolfing
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zhiying Guo
- Soil Subcenter of Chinese Ecological Research Network, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Ruirui Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Meng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Zhongpei Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008 People’s Republic of China
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17
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Zhang X, Qi L, Li W, Hu BX, Dai Z. Bacterial community variations with salinity in the saltwater-intruded estuarine aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142423. [PMID: 33017763 DOI: 10.1016/j.scitotenv.2020.142423] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Bacterial community has been significantly enrolled in the biogeochemical cycling of the coastal subsurface ecosystem. The bacterial community variations with salinity have been extensively investigated in the surface environment, such as lake, soil, and estuary, but not in the subsurface environment. Here we explore the responses of bacterial populations to the salinity and other environmental factors (EFs) by considering both the abundant and rare sub-community in a coastal Holocene groundwater system. Our study results indicate that the bacterial diversity was independent of the salinity in both the abundance and rare sub-community. Besides diversity, no flourishing of abundant bacteria relative abundance is observed with increasing or decreasing salinity. Yet the rare taxa exhibit a bio-growth with salinity, which has a significant correlation (p < 0.001) with sulfate concentration. The responses of the abundant sub-community taxa to nutrients, temperature, pH, and dissolved oxygen are insensitive. However, the correlation between δ18O, δD and the entire community diversity is significant, which demonstrates the bacterial community is affected by the groundwater origin. Besides, not all the species in one class or order are necessarily shaped by the same factor. To quantify the impact of EFs on the community properties, analyses in different taxonomic levels is suggested. These findings imply that the spatial organization of microbial communities is complicated and influenced by multiple factors on a regional scale. The investigated results are useful for understanding biogeochemical processes in the coastal groundwater.
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Affiliation(s)
- Xiaoying Zhang
- College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Linlin Qi
- College of Construction Engineering, Jilin University, Changchun 130026, China
| | - Wenming Li
- Xi'an Center of China Geological Survey, Xi'an 710054, China
| | - Bill X Hu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangdong 510632, China.
| | - Zhenxue Dai
- College of Construction Engineering, Jilin University, Changchun 130026, China.
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18
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Nguyen NHA, Špánek R, Falagan-Lotsch P, Ševců A. Impact of Zero-Valent Iron on Freshwater Bacterioplankton Metabolism as Predicted from 16S rRNA Gene Sequence Libraries. Curr Microbiol 2021; 78:979-991. [PMID: 33521895 DOI: 10.1007/s00284-021-02362-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 01/10/2021] [Indexed: 11/25/2022]
Abstract
The application of zero-valent iron particles (ZVI) for the treatment of heavily polluted environment and its biological effects have been studied for at least two decades. Still, information on the impact on bacterial metabolic pathways is lacking. This study describes the effect of microscale and nanoscale ZVI (mZVI and nZVI) on the abundance of different metabolic pathways in freshwater bacterial communities. The metabolic pathways were inferred from metabolism modelling based on 16S rRNA gene sequence data using paprica pipeline. The nZVI changed the abundance of numerous metabolic pathways compared to a less influencing mZVI. We identified the 50 most affected pathways, where 31 were related to degradation, 17 to biosynthesis, and 2 to detoxification. The linkage between pathways was two times higher in nZVI samples compared to mZVI, and was specifically higher considering the arsenate detoxification II pathway. Limnohabitans and Roseiflexus were linked to the same pathways in both nZVI and mZVI. The prediction of metabolic pathways increases our knowledge of the impacts of nZVI and mZVI on freshwater bacterioplankton.
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Affiliation(s)
- Nhung H A Nguyen
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec (TUL), Studentská 2, 46117, Liberec, Czech Republic.
| | - Roman Špánek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec (TUL), Studentská 2, 46117, Liberec, Czech Republic. .,Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec (TUL), Studentská 2, 46117, Liberec, Czech Republic.
| | - Priscila Falagan-Lotsch
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.,Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec (TUL), Studentská 2, 46117, Liberec, Czech Republic.
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19
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Almeida AM, Filho JEA, Souza RM. In bromeliad phytotelma, anthropic disturbance does not affect the nematode trophic structure. J Nematol 2020; 52:e2020-101. [PMID: 33829184 PMCID: PMC8015329 DOI: 10.21307/jofnem-2020-101] [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: 01/09/2020] [Indexed: 11/11/2022] Open
Abstract
Phytotelmata (sing. phytotelma) are plant-associated reservoirs of rainwater and organic debris. These freshwater ecosystems are found in tree and bamboo holes, pitcher plants, and tank-forming bromeliads. Some studies suggest that anthropic disturbance (AD) may change the physico-chemical properties (PCPs) of the water retained in the phytotelma, and indirectly impact its biota. Hence, new AD-bioindicators could be found in the phytotelma biota. To test this hypothesis, three areas of Atlantic Forest were selected, distinct only by the level of long-term AD. In these areas, we monitored the nematode trophic structure and the water PCPs in the bromeliad Neoregelia cruenta during two years (eight seasons). Significant differences among areas were found in some seasons for total nematode abundance and/or the abundance of some trophic groups, but no pattern emerged relative to the level of AD. Anthropic disturbance did not impact nematode trophic structure possibly because the water PCPs remained fairly similar in all three areas. Our results do not corroborate previous reports that AD alters phytotelma water. On the other hand, our findings support previous studies suggesting that nematodes inhabiting bromeliad phytotelma are not good candidates for AD-bioindicators.
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Affiliation(s)
- Alexandre Macedo Almeida
- Grupo de Pesquisa em Nematologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Campos dos Goytacazes (RJ), 28015-602, Brazil
| | | | - Ricardo Moreira Souza
- Grupo de Pesquisa em Nematologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, Campos dos Goytacazes (RJ), 28015-602, Brazil
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20
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Simão TLL, Utz LRP, Dias R, Giongo A, Triplett EW, Eizirik E. Remarkably Complex Microbial Community Composition in Bromeliad Tank Waters Revealed by eDNA Metabarcoding. J Eukaryot Microbiol 2020; 67:593-607. [PMID: 32562451 DOI: 10.1111/jeu.12814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/04/2020] [Accepted: 06/04/2020] [Indexed: 11/29/2022]
Abstract
To investigate patterns of biotic community composition at different spatial scales and biological contexts, we used environmental DNA metabarcoding to characterize eukaryotic and prokaryotic assemblages present in the phytotelmata of three bromeliad species (Aechmea gamosepala, Vriesea friburgensis, and Vriesea platynema) at a single Atlantic Forest site in southern Brazil. We sampled multiple individuals per species and multiple tanks from each individual, totalizing 30 samples. We observed very high levels of diversity in these communities, and remarkable variation across individuals and even among tanks from the same individual. The alpha diversity was higher for prokaryotes than eukaryotes, especially for A. gamosepala and V. platynema samples. Some biotic components appeared to be species-specific, while most of the biota was shared among species, but varied substantially in frequency among samples. Interestingly, V. friburgensis communities (which were sampled at nearby locations) tended to be more heterogeneous across samples, for both eukaryotes and prokaryotes. The opposite was true for V. platynema, whose samples were more broadly spaced but whose communities were more similar to each other. Our results indicate that additional attention should be devoted to within-individual heterogeneity when assessing bromeliad phytotelmata biodiversity, and highlight the complexity of the biotic assemblages gathered in these unique habitats.
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Affiliation(s)
- Taiz L L Simão
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Laura R P Utz
- Laboratório de Ecologia Aquática, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Raquel Dias
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California, 92037, USA
| | - Adriana Giongo
- Instituto do Petróleo e Recursos Naturais, PUCRS, Av. Ipiranga 6681, prédio 96J, Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, 1052 Museum Road, P.O. Box 110700, Gainesville, Florida, 32608, USA
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências da Saúde e da Vida, PUCRS, Av. Ipiranga, 6681, prédio 12., Porto Alegre, Rio Grande do Sul, 90619-900, Brazil
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Duarte CM, Røstad A, Michoud G, Barozzi A, Merlino G, Delgado-Huertas A, Hession BC, Mallon FL, Afifi AM, Daffonchio D. Discovery of Afifi, the shallowest and southernmost brine pool reported in the Red Sea. Sci Rep 2020; 10:910. [PMID: 31969577 PMCID: PMC6976674 DOI: 10.1038/s41598-020-57416-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/31/2019] [Indexed: 12/14/2022] Open
Abstract
The previously uncharted Afifi brine pool was discovered in the eastern shelf of the southern Red Sea. It is the shallowest brine basin yet reported in the Red Sea (depth range: 353.0 to 400.5 m). It presents a highly saline (228 g/L), thalassohaline, cold (23.3 °C), anoxic brine, inhabited by the bacterial classes KB1, Bacteroidia and Clostridia and the archaeal classes Methanobacteria and Deep Sea Euryarcheota Group. Functional assignments deduced from the taxonomy indicate methanogenesis and sulfur respiration to be important metabolic processes in this environment. The Afifi brine was remarkably enriched in dissolved inorganic carbon due to microbial respiration and in dissolved nitrogen, derived from anammox processes and denitrification, according to high δ15N values (+6.88‰, AIR). The Afifi brine show a linear increase in δ18O and δD relative to seawater that differs from the others Red Sea brine pools, indicating a non-hydrothermal origin, compatible with enrichment in evaporitic environments. Afifi brine was probably formed by venting of fossil connate waters from the evaporitic sediments beneath the seafloor, with a possible contribution from the dehydration of gypsum to anhydrite. Such origin is unique among the known Red Sea brine pools.
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Affiliation(s)
- Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Anders Røstad
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alan Barozzi
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Giuseppe Merlino
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Antonio Delgado-Huertas
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Avda. de las Palmeras 4, 18100, Armilla, Spain
| | - Brian C Hession
- Coastal and Marine Resources Core Lab (CMOR), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Francis L Mallon
- Coastal and Marine Resources Core Lab (CMOR), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Abdulakader M Afifi
- Ali I. Al-Naimi Petroleum Engineering Research Center (ANPERC), Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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22
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23
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Wang CY, Zhou X, Guo D, Zhao JH, Yan L, Feng GZ, Gao Q, Yu H, Zhao LP. Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01529-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Abstract
Purpose
To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil.
Method
A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions.
Result
The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.
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24
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Seasonal Physiological Parameters and Phytotelmata Bacterial Diversity of Two Bromeliad Species (Aechmea gamosepala and Vriesea platynema) from the Atlantic Forest of Southern Brazil. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11070111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at an Atlantic Forest site and used 16S rDNA metabarcoding to survey the microbial communities inhabiting their tanks. We observed that levels of some nutrients (e.g., nitrogen) varied across seasons consistently in both species, while others (e.g., phenolic compounds) presented considerable differences between the two bromeliads. In contrast, patterns of tank microbial diversity did not follow a similar temporal trend. There was extensive variation in microbial composition among samples, which included intra-specific differences but also some consistent differences between the two bromeliads. For example, Citrobacter, Klebsiella and Pantoea presented significantly different abundances in the two species. Interestingly, the dominant bacterial genera in both species included Pseudomonas and Enterobacter, which have been reported to include plant-beneficial species. Overall, our data contribute to the characterization of the nutritional status of Atlantic Forest bromeliads and the composition of their prokaryotic communities, laying the foundation for detailed investigations targeting the ecological interactions between these plants and their associated microbes.
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Deng J, Zhang Y, Yin Y, Zhu X, Zhu W, Zhou Y. Comparison of soil bacterial community and functional characteristics following afforestation in the semi-arid areas. PeerJ 2019; 7:e7141. [PMID: 31275750 PMCID: PMC6598672 DOI: 10.7717/peerj.7141] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023] Open
Abstract
Changes in soil bacterial communities, which are crucial for the assessment of ecological restoration in Chinese plantations, have never been studied in the "Three North Shelterbelt" project in the semi-arid areas. We used high-throughput sequencing of the 16S rDNA gene to investigate the soil bacterial community diversity, structure, and functional characteristics in three plantation forests, including Populus × canadensis Moench (PC), Pinus sylvestris var. mongolica (PS), and Pinus tabuliformis (PT). In addition, soil environment factors were measured. There were distinct differences in soil characteristics among different plantation forests. Compared to PS and PT, PC had a higher soil pH, dissolved organic carbon (DOC), and available P, as well as a lower C/N ratio. Furthermore, afforestation with different tree species significantly altered the abundance of Proteobacteria, and Chloroflexi in the soil, and its influence on the bacterial diversity indices. The bacterial community compositions and functional groups related to C and N cycling from PS, and PT were grouped tightly, indicating that the soil bacterial phylogenetic distance of PS and PT were closer than that between PS plus PT and PC. Our results implied that the soil characteristics, as well as the diversity, compositions and functions related to C and N cycling of soil bacterial community obviously differed from the following afforestation, especially between PC and PS plus PT, which in turn enormously established the correlation between the soil microbial community characteristics and the afforestation tree species.
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Affiliation(s)
- Jiaojiao Deng
- College of Forestry, Shenyang Agriculture University, Shenyang, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Yan Zhang
- College of Forestry, Shenyang Agriculture University, Shenyang, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - You Yin
- College of Forestry, Shenyang Agriculture University, Shenyang, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Xu Zhu
- LliaoNing JianZhu Vocational College, Liaoyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
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26
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Zhang M, Riaz M, Zhang L, El-Desouki Z, Jiang C. Biochar Induces Changes to Basic Soil Properties and Bacterial Communities of Different Soils to Varying Degrees at 25 mm Rainfall: More Effective on Acidic Soils. Front Microbiol 2019; 10:1321. [PMID: 31249563 PMCID: PMC6582450 DOI: 10.3389/fmicb.2019.01321] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/27/2019] [Indexed: 02/04/2023] Open
Abstract
Biochar and chemical fertilizer have been widely used in agriculture. Most studies have proved that they not only alter soil nutrient content, but also have an impact on soil microbial communities. However, the effects of biochar and chemical fertilizer application on the overall bacterial community in different soil types under rainfall conditions are not yet understood. We took rainfall as a fixed influencing factor and selected four typical soils of China to investigate the bacterial effects of biochar and chemical fertilizer at 25 mm rainfall, and to identify specific differential bacteria and their functions, and to explore the changes of the bacterial community structure of different soil types. The depth of simulated rainfall was 25 mm each time. Yellow-brown soil, fluvo-aquic soil, lou soil, and black soil were chosen for experiment and each soil was divided into four treatments, included non-biochar and non-fertilizer (CK), fertilizer alone (F), biochar alone (C), and combination of biochar and fertilizer (FC). The results indicated that biochar and fertilizer have a more significant effect on bacterial communities in acidic soils. The amendment of biochar and fertilizer alone or together identified 3 (f_Oxalobacteraceae, f_Solibacteraceae_Subgroup_3, f_Sphingomonadaceae), 5 (f_Chitinophagaceae, f_Comamonadaceae, f_Geobacteraceae, f_norank_o_SC-I-84, f_norank_c_OPB35_soil_group), 1 (f_Blastocatellaceae_Subgroup_4) and 0 differential bacteria in yellow-brown soil, fluvo-aquic soil, lou soil, and black soil by statistical test. In yellow-brown soil, the application of biochar alone increased the relative abundance of potential pathogens within the Sphingomonadaceae and reduced the relative abundance of beneficial bacteria in Solibacteraceae, but the addition of biochar and fertilizer together increased the relative abundance of some beneficial bacteria in Oxalobacteraceae. In fluvo-aquic soil, both biochar, and chemical fertilizers promoted the relative abundance of some beneficial bacteria belonging to Chitinophagaceae, Comamonadaceae, and Geobacteraceae that may be involved in nutrient cycling, degradation of plant residues and increase of metal tolerance. The interactions between acidic soil bacterial communities and measured soil parameters including pH, organic matter were found to be statistically significant. Results from this study revealed that it is necessary to formulate biochar and fertilizer application schemes based on different soil types.
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Affiliation(s)
- Mengyang Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Lin Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Zeinab El-Desouki
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China.,Department of Soil Sciences, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
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27
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Zhang J, Chen M, Huang J, Guo X, Zhang Y, Liu D, Wu R, He H, Wang J. Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea. PLoS One 2019; 14:e0215328. [PMID: 30973915 PMCID: PMC6459509 DOI: 10.1371/journal.pone.0215328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023] Open
Abstract
The nitrogen (N) cycle is closely related to the stability of marine ecosystems. Microbial communities have been directly linked to marine N-cycling processes. However, systematic research on the bacterial community composition and diversity involved in N cycles in different seas is lacking. In this study, microbial diversity in the Bohai Sea (BHS), Yellow Sea (YS) and South China Sea (SCS) was surveyed by targeting the hypervariable V4 regions of the 16S rRNA gene using next-generation sequencing (NGS) technology. A total of 2,505,721 clean reads and 15,307 operational taxonomic units (OTUs) were obtained from 86 sediment samples from the three studied China seas. LEfSe analysis demonstrated that the SCS had more abundant microbial taxa than the BHS and YS. Diversity indices demonstrated that Proteobacteria and Planctomycetes were the dominant phyla in all three China seas. Canonical correspondence analysis (CCA) indicated that pH (P = 0.034) was the principal determining factors, while the organic matter content, depth and temperature had a minor correlated with the variations in sedimentary microbial community distribution. Cluster and functional analyses of microbial communities showed that chemoheterotrophic and aerobic chemoheterotrophic microorganisms widely exist in these three seas. Further research found that the cultivable protease-producing bacteria were mainly affiliated with the phyla Proteobacteria, Firmicutes and Bacteroidetes. It was very clear that Pseudoalteromonadaceae possessed the highest relative abundance in the three sea areas. The predominant protease-producing genera were Pseudoalteromonas and Bacillus. These results shed light on the differences in bacterial community composition, especially protease-producing bacteria, in these three China seas.
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Affiliation(s)
- Jiang Zhang
- School of Life Science, Central South University, Changsha, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, China
| | - Jiafeng Huang
- School of Life Science, Central South University, Changsha, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, China
| | - Yanjiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Dan Liu
- School of Life Science, Central South University, Changsha, China
| | - Ribang Wu
- School of Life Science, Central South University, Changsha, China
| | - Hailun He
- School of Life Science, Central South University, Changsha, China
- * E-mail: (HH); (GW)
| | - Jun Wang
- School of Life Science, Central South University, Changsha, China
- Sanway Gene Technology Inc., Changsha, China
- * E-mail: (HH); (GW)
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28
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Pan H, Yang X, Zhong Y, Xu M, Sun G. Response of environmental variables and microbial community to sodium percarbonate addition to contaminated sediment. CHEMOSPHERE 2018; 211:500-509. [PMID: 30086526 DOI: 10.1016/j.chemosphere.2018.07.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Sodium percarbonate (SPC) is a common reagent used for in situ remediation of contaminated soil. Current studies focus on the effects of SPC on pollutant removal; however, a knowledge gap exists for the biochemical process following SPC addition. In this study, a microcosm batch experiment was conducted to investigate the residual effect caused by different doses of SPC addition on native microbial communities, as well as on the environmental variables of contaminated sediments. The obtained results showed that the more SPC was added, the more dissolved matters were generated and the oxidation-reduction potential was lowered. Furthermore, the metabolic activities of the microbial community were enhanced and the microbial community structure responded differently to different SPC doses: the microbes that increased at high SPC dose mainly belonged to the phylum Firmicutes, the class Clostridia, and the genera Petrimonas and Proteiniclasticum. The microbes that increased at medium SPC dose mainly belonged to the class Alphaproteobacteria and the genus Brevundimonas. In contrast, vulnerable microbes mainly belonged to the phylum Acidobacteria, the class Caldisericia, Holophagae, and the genus Sulfuricurvum. Microbes capable of fermentation, ureolysis, and chemohetrotrophy increased. These results indicate that SPC addition could indirectly provide both electron acceptors and donors, thus improving the metabolic activities of the microorganisms in the contaminated sediment. Furthermore, the utilized SPC dose should be considered to achieve the optimal benefit for in situ remediation. This study forms a valuable reference for the application of SPC in ecological engineering.
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Affiliation(s)
- Hanping Pan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Yuming Zhong
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
| | - Guoping Sun
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, 58th Building, 100 Central Xianlie Road, Guangzhou 510070, China.
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29
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Cai J, Bai C, Tang X, Dai J, Gong Y, Hu Y, Shao K, Zhou L, Gao G. Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31543-31557. [PMID: 30206827 DOI: 10.1007/s11356-018-2987-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
While the important roles of microbial communities in oceanic hypoxic zones were beginning to be understood, little is known about microbial community associated with this phenomenon in shallow lakes. To address this deficit, both the bacterial and microbial eukaryotic communities of an ephemeral hypoxic area of Taihu Lake were characterized. The hypoxia provided nutritional niches for various bacteria, which results in high abundance and diversity. Specific bacterial groups, such as vadinBC27 subgroup of Bacteroidetes, Burkholderiales, Rhodocyclales, Pseudomonas, and Parcubacteria, were dominated in hypoxic sites and relevant to the fermentation, denitrification, nitrification, and sulfur metabolism. Conversely, most of microbial eukaryotes disappeared along with the decline of DO. An unexpected dominance of fungi was observed during hypoxia, which partly explained by the accumulation of toxic algae. Mucor was the single dominant genus in the hypoxic zone. We proposed that this group might cooperate with bacterial communities in the anaerobic degradation of algal biomass and woody materials. Generally, the hypoxic microbiome in shallow lakes is mainly involved in fermentative metabolism depending on phytodetritus and is potentially influenced by terrestrial sources. This study provided new insights into the unique microbiome in short-term hypoxia in shallow lakes and lays the foundation for studies that will enhance our understanding of the microbial players associated with hypoxia and their adaption strategy on the global scale.
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Affiliation(s)
- Jian Cai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Chengrong Bai
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Jiangyu Dai
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, 210029, People's Republic of China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Lei Zhou
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
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30
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Zhang X, Hu BX, Ren H, Zhang J. Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:518-528. [PMID: 29579663 DOI: 10.1016/j.scitotenv.2018.03.158] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 05/25/2023]
Abstract
The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity.
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Affiliation(s)
- Xiaoying Zhang
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; Department of Ecology, Jinan University, 510632 Guangzhou, China.
| | - Bill X Hu
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; School of Water Resources and Environment, China University of Geosciences (Beijing), 100083 Beijing, China.
| | - Hejun Ren
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 130021 Changchun, China
| | - Jin Zhang
- Institute of Urban Water Management, Technische Universität Dresden, 01062 Dresden, Germany
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31
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Antiqueira PAP, Petchey OL, Dos Santos VP, de Oliveira VM, Romero GQ. Environmental change and predator diversity drive alpha and beta diversity in freshwater macro and microorganisms. GLOBAL CHANGE BIOLOGY 2018; 24:3715-3728. [PMID: 29772087 DOI: 10.1111/gcb.14314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/23/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
Global biodiversity is eroding due to anthropogenic causes, such as climate change, habitat loss, and trophic simplification of biological communities. Most studies address only isolated causes within a single group of organisms; however, biological groups of different trophic levels may respond in particular ways to different environmental impacts. Our study used natural microcosms to investigate the predicted individual and interactive effects of warming, changes in top predator diversity, and habitat size on the alpha and beta diversity of macrofauna, microfauna, and bacteria. Alpha diversity (i.e., richness within each bromeliad) generally explained a larger proportion of the gamma diversity (partitioned in alpha and beta diversity). Overall, dissimilarity between communities occurred due to species turnover and not species loss (nestedness). Nevertheless, the three biological groups responded differently to each environmental stressor. Microfauna were the most sensitive group, with alpha and beta diversity being affected by environmental changes (warming and habitat size) and trophic structure (diversity of top predators). Macrofauna alpha and beta diversity was sensitive to changes in predator diversity and habitat size, but not warming. In contrast, the bacterial community was not influenced by the treatments. The community of each biological group was not mutually concordant with the environmental and trophic changes. Our results demonstrate that distinct anthropogenic impacts differentially affect the components of macro and microorganism diversity through direct and indirect effects (i.e., bottom-up and top-down effects). Therefore, a multitrophic and multispecies approach is necessary to assess the effects of different anthropogenic impacts on biodiversity.
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Affiliation(s)
- Pablo Augusto P Antiqueira
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Laboratory of Multitrophic Interactions and Biodiversity, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Owen L Petchey
- Department for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Viviane Piccin Dos Santos
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, SP, Brazil
| | - Valéria Maia de Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas, Paulínia, SP, Brazil
| | - Gustavo Quevedo Romero
- Laboratory of Multitrophic Interactions and Biodiversity, Institute of Biology, University of Campinas, Campinas, SP, Brazil
- Departamento de Biologia Animal, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- Brazilian Research Network on Climate Change (Rede Clima), São Paulo, Brazil
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Pires APF, Srivastava DS, Marino NAC, MacDonald AAM, Figueiredo‐Barros MP, Farjalla VF. Interactive effects of climate change and biodiversity loss on ecosystem functioning. Ecology 2018; 99:1203-1213. [DOI: 10.1002/ecy.2202] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/22/2018] [Accepted: 02/15/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Aliny P. F. Pires
- Departamento de Ecologia Instituto de Biologia Universidade Federal do Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil
- Fundação Brasileira para o Desenvolvimento Sustentável Rio de Janeiro Rio de Janeiro Brazil
- Brazilian Research Network on Climate Change ‐ Rede Clima Instituto Nacional de Pesquisas Espaciais São José dos Campos Sao Paulo Brazil
| | - Diane S. Srivastava
- Department of Zoology and Biodiversity Research Centre University of British Columbia 6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
| | - Nicholas A. C. Marino
- Departamento de Ecologia Instituto de Biologia Universidade Federal do Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil
| | - A. Andrew M. MacDonald
- Department of Zoology and Biodiversity Research Centre University of British Columbia 6270 University Boulevard Vancouver British Columbia V6T1Z4 Canada
| | - Marcos Paulo Figueiredo‐Barros
- Núcleo em Ecologia e Desenvolvimento Socio‐Ambiental de Macaé (NUPEM/UFRJ) Universidade Federal do Rio de Janeiro Macaé Rio de Janeiro Brazil
| | - Vinicius F. Farjalla
- Departamento de Ecologia Instituto de Biologia Universidade Federal do Rio de Janeiro Rio de Janeiro Rio de Janeiro Brazil
- Brazilian Research Network on Climate Change ‐ Rede Clima Instituto Nacional de Pesquisas Espaciais São José dos Campos Sao Paulo Brazil
- Laboratorio Internacional en Cambio Global – LINCGlobal Sunnyvale California USA
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Martinson GO, Pommerenke B, Brandt FB, Homeier J, Burneo JI, Conrad R. Hydrogenotrophic methanogenesis is the dominant methanogenic pathway in neotropical tank bromeliad wetlands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:33-39. [PMID: 29124879 DOI: 10.1111/1758-2229.12602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH4 -cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH4 production potential, stable carbon isotope fractionation and pathway of CH4 formation. The archaeal community composition was dominated by methanogens and differed between bromeliad functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens and hydrogenotrophic methanogenesis was the dominant methanogenic pathway among all bromeliads. The relative abundance of aceticlastic Methanosaetaceae and the relative contribution of aceticlastic methanogenesis increased in type-I tank bromeliads probably due to more oxic conditions in type-I than in type-II bromeliads leading to the previously observed lower in situ CH4 emissions from type-I tank bromeliads but to higher CH4 production potentials in type-I tank bromeliad slurries.
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Affiliation(s)
- Guntars O Martinson
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Karl-von-Frisch-Straße 10, Germany
| | - Bianca Pommerenke
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Karl-von-Frisch-Straße 10, Germany
| | - Franziska B Brandt
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Karl-von-Frisch-Straße 10, Germany
| | - Jürgen Homeier
- Albrecht von Haller Institute of Plant Sciences, Georg August University Goettingen, Goettingen, Germany
| | - Juan I Burneo
- Departamento de Química y Ciencias Exactas, Universidad Técnica Particular de Loja, Ecuador
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Karl-von-Frisch-Straße 10, Germany
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Rodriguez-Nuñez KM, Rullan-Cardec JM, Rios-Velazquez C. The metagenome of bromeliads phytotelma in Puerto Rico. Data Brief 2017; 16:19-22. [PMID: 29167815 PMCID: PMC5686464 DOI: 10.1016/j.dib.2017.10.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/11/2017] [Accepted: 10/26/2017] [Indexed: 11/26/2022] Open
Abstract
Bromeliads tank water or phytotelma is an eutrophic microenvironment where microorganisms have evolved to resist sudden changes in pH and nutritional competition. Metagenomics studies have been poorly studied in bromeliads and environmental DNA (eDNA) characterization for its microenvironment is deficient in Puerto Rico. Therefore, the data represents the microbial communities inhabiting bromeliads phytotelma. eDNA was extracted using Metagenomic DNA Isolation Kit for Water. Next-Generation-Sequencing technology (Illumina MiSeq) was used for sequencing the isolated eDNA. This data provides an insight about diversity and functional depiction of microorganisms inhabiting bromeliads phytotelma. The data of this metagenome is available in the BioSample Submission Portal as Bioproject PRJNA39461 and Sequence Read Archive (SRA) accession number SRP114300. MG-RAST metagenomic analysis server is located under the study ID mgp79812.
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Affiliation(s)
- Kiara M Rodriguez-Nuñez
- Biology Department, University of Puerto Rico at Mayagüez, Call Box 9000, Mayagüez, PR 00681-9000, United States
| | - Jesie M Rullan-Cardec
- Biology Department, University of Puerto Rico at Mayagüez, Call Box 9000, Mayagüez, PR 00681-9000, United States
| | - Carlos Rios-Velazquez
- Biology Department, University of Puerto Rico at Mayagüez, Call Box 9000, Mayagüez, PR 00681-9000, United States
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