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Wang Y, Hu Y, Liu Y, Chen Q, Xu J, Zhang F, Mao J, Shi Q, He C, Cai R, Lønborg C, Liu L, Guo A, Jiao N, Zheng Q. Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172003. [PMID: 38569948 DOI: 10.1016/j.scitotenv.2024.172003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China; College of Environmental and Ecology, Xiamen University, Xiamen, China
| | - Yuxing Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jinxin Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Fei Zhang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, China
| | - Jinhua Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Quan Shi
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Chen He
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Christian Lønborg
- Department of Ecoscience, Section for Marine Diversity and Experimental Ecology, University of Aarhus, Roskilde, Denmark
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xiamen, China
| | - Aixing Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
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Wang Y, Su N, Lian E, Wang R. Spatial heterogeneity of sedimentary organic matter sources in the Yangtze River estuary: Implications from fatty acid biomarkers. MARINE POLLUTION BULLETIN 2024; 201:116249. [PMID: 38484535 DOI: 10.1016/j.marpolbul.2024.116249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/26/2024] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
This study investigated the sources of sedimentary organic matter (OM) in the Yangtze River estuary (YRE), using multiple biomarkers. The results of stable carbon isotope (δ13C) and total organic carbon to nitrogen ratio (TOC/TN) suggests the contribution of marine-derived OM significantly increased seawards, while fatty acid (FA) composition provides more specific information on OM sources. In total, 30 components of FAs were identified at the studied 17 sites, which mainly composed of phytoplankton FA, followed by ubiquitous FA and bacterial FA, while terrestrial FA contributed less to the total FAs. Under the strong impacts of the large physicochemical gradients in the YRE, TOC, TN and FA components showed higher concentrations in the estuary mixing zone (especially within the turbidity maximum zone), attributing to their strong binding with OM-enriched fine particles. The spatial heterogeneity of sedimentary OM sources was highly impacted by salinity and Chl-a, as well as bacteria-mediated OM degradation.
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Affiliation(s)
- Yunhui Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Ni Su
- State Key Laboratory of Marine Geology, School of Ocean and Earth Science, Tongji University, Shanghai 200092, PR China
| | - Ergang Lian
- State Key Laboratory of Marine Geology, School of Ocean and Earth Science, Tongji University, Shanghai 200092, PR China; Research Center for Monitoring and Environmental Sciences, Taihu Basin & East China Sea Ecological Environment Supervision and Administration Authority, Ministry of Ecology and Environment, Shanghai 200120, PR China
| | - Rui Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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McNichol SM, Sanchez-Quete F, Loeb SK, Teske AP, Shah Walter SR, Mahmoudi N. Dynamics of carbon substrate competition among heterotrophic microorganisms. THE ISME JOURNAL 2024; 18:wrae018. [PMID: 38366177 PMCID: PMC10942773 DOI: 10.1093/ismejo/wrae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/06/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Growing evidence suggests that interactions among heterotrophic microorganisms influence the efficiency and rate of organic matter turnover. These interactions are dynamic and shaped by the composition and availability of resources in their surrounding environment. Heterotrophic microorganisms inhabiting marine environments often encounter fluctuations in the quality and quantity of carbon inputs, ranging from simple sugars to large, complex compounds. Here, we experimentally tested how the chemical complexity of carbon substrates affects competition and growth dynamics between two heterotrophic marine isolates. We tracked cell density using species-specific polymerase chain reaction (PCR) assays and measured rates of microbial CO2 production along with associated isotopic signatures (13C and 14C) to quantify the impact of these interactions on organic matter remineralization. The observed cell densities revealed substrate-driven interactions: one species exhibited a competitive advantage and quickly outgrew the other when incubated with a labile compound whereas both species seemed to coexist harmoniously in the presence of more complex organic matter. Rates of CO2 respiration revealed that coincubation of these isolates enhanced organic matter turnover, sometimes by nearly 2-fold, compared to their incubation as mono-cultures. Isotopic signatures of respired CO2 indicated that coincubation resulted in a greater remineralization of macromolecular organic matter. These results demonstrate that simple substrates promote competition whereas high substrate complexity reduces competitiveness and promotes the partitioning of degradative activities into distinct niches, facilitating coordinated utilization of the carbon pool. Taken together, this study yields new insight into how the quality of organic matter plays a pivotal role in determining microbial interactions within marine environments.
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Affiliation(s)
- Samuel M McNichol
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
| | - Fernando Sanchez-Quete
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Stephanie K Loeb
- Department of Civil Engineering, McGill University, 817 Rue Sherbrooke Ouest, Montréal, Quebec H3A 0C3, Canada
| | - Andreas P Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC 27599, United States
| | - Sunita R Shah Walter
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd, Lewes, DE 19958, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, 3450 University St, Montréal, Quebec H3A 0E8, Canada
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Mahmoudi N, Wilhelm RC. Can we manage microbial systems to enhance carbon storage? Environ Microbiol 2023; 25:3011-3018. [PMID: 37431673 DOI: 10.1111/1462-2920.16462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Climate change is an urgent environmental issue with wide-ranging impacts on ecosystems and society. Microbes are instrumental in maintaining the balance between carbon (C) accumulation and loss in the biosphere, actively regulating greenhouse gas fluxes from vast reservoirs of organic C stored in soils, sediments and oceans. Heterotrophic microbes exhibit varying capacities to access, degrade and metabolise organic C-leading to variations in remineralisation and turnover rates. The present challenge lies in effectively translating this accumulated knowledge into strategies that effectively steer the fate of organic C towards prolonged sequestration. In this article, we discuss three ecological scenarios that offer potential avenues for shaping C turnover rates in the environment. Specifically, we explore the promotion of slow-cycling microbial byproducts, the facilitation of higher carbon use efficiency, and the influence of biotic interactions. The ability to harness and control these processes relies on the integration of ecological principles and management practices, combined with advances in economically viable technologies to effectively manage microbial systems in the environment.
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Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, Quebec, Canada
| | - Roland C Wilhelm
- Department of Agronomy, Lilly Hall of Life Sciences, Purdue University, West Lafayette, Indiana, USA
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Mindorff LM, Mahmoudi N, Hepditch SLJ, Langlois VS, Alam S, Martel R, Ahad JME. Isotopic and microbial evidence for biodegradation of diluted bitumen in the unsaturated zone. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 322:121170. [PMID: 36736816 DOI: 10.1016/j.envpol.2023.121170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
The oil sands region in Western Canada is one of the world's largest proven oil reserves. To facilitate pipeline transport, highly viscous oil sands bitumen is blended with lighter hydrocarbon fractions to produce diluted bitumen (dilbit). Anticipated increases in dilbit production and transport raise the risk of inland spills. To understand the behaviour of dilbit in the unsaturated or vadose zone following a surface spill, we ran parallel dilbit and conventional heavy crude exposures, along with an untreated control, using large soil-filled columns over 104 days. Phospholipid fatty acids (PLFAs), biomarkers for the active microbial population, were extracted from column soil cores. Stable carbon isotope contents (δ13C) of individual PLFAs and radiocarbon contents (Δ14C) of bulk PLFAs were characterized over the course of the experiment. The Δ14CPLFA values in soils impacted by dilbit (-221.1 to -54.7‰) and conventional heavy crude (-259.4 to -97.9‰) indicated similar levels of microbial uptake of fossil carbon. In contrast, Δ14CPLFA values in the control column (-46.1 to +53.7‰) reflected assimilation of more recently fixed organic carbon. Sequencing of 16S ribosomal RNA genes extracted from soil cores revealed a significant increase in the relative abundance of Polaromonas, a known hydrocarbon-degrader, following exposure to both types of oil. This study demonstrates that in the first several months following a surface spill, dilbit has a similar potential for biodegradation by a native shallow subsurface microbial community as conventional heavy crude oil.
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Affiliation(s)
- Leah M Mindorff
- Department of Earth and Planetary Sciences, McGill University, Montréal, QC, H3A 0E8, Canada; Geological Survey of Canada, Natural Resources Canada, Québec, QC, G1K 9A9, Canada
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montréal, QC, H3A 0E8, Canada
| | - Scott L J Hepditch
- Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, G1K 9A9, Canada
| | - Valerie S Langlois
- Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, G1K 9A9, Canada
| | - Samrat Alam
- Geological Survey of Canada, Natural Resources Canada, Québec, QC, G1K 9A9, Canada
| | - Richard Martel
- Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, Québec, QC, G1K 9A9, Canada
| | - Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec, QC, G1K 9A9, Canada.
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Zhang Y, Liu J, Kang L, Gu Y, Qu L, Liu B, Sun L, Xing M, Ma Z, Sun Y. Temporal variation of mineralization rates and its influence on carbon storage over the last 50 years in Bohai Bay, China. MARINE POLLUTION BULLETIN 2023; 188:114624. [PMID: 36736251 DOI: 10.1016/j.marpolbul.2023.114624] [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: 07/17/2022] [Revised: 12/23/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Recorded information on marine sediments is affected by mineralization. In this study, we collected sediment samples from Bohai Bay, where human interference is typically high. Overall, the CO2 fluxes in the columnar sediments decreased with increasing depth. The change in constants revealed a "C-curve" in which the mineralization rate first decreased significantly (i.e., from the 2020s to the 1980s) and subsequently increased slowly (i.e., from the 1980s to 1965). This may be explained by the fact that sediments from the 1980s-2020s were markedly influenced by the sedimentation rate, whereas sediments from the 1960s-1980s were predominantly influenced by microbial action. The loss of organic carbon due to mineralization accounted for approximately 15-20 % of the initial total organic carbon; therefore, when performing an inversion of the historical environment change using information derived from organic carbon in marine sediments, the influence of mineralization on this information should be fully considered.
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Affiliation(s)
- Yan Zhang
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Jingjing Liu
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China; Tianjin Lishen Battery Joint-stock Co., Ltd., Binhai New Area, Tianjin 300384, China
| | - Lei Kang
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China.
| | - Yingnan Gu
- Tianjin Huanke Testing Technology Co., Ltd., Nankai, Tianjin 300191, China
| | - Long Qu
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Bao Liu
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Lina Sun
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Meinan Xing
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Zhe Ma
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
| | - Ying Sun
- Tianjin Academy of Eco-Environmental Sciences, Nankai, Tianjin 300191, China
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Gonzalez-Nayeck AC, Mohr W, Tang T, Sattin S, Parenteau MN, Jahnke LL, Pearson A. Absence of canonical trophic levels in a microbial mat. GEOBIOLOGY 2022; 20:726-740. [PMID: 35831948 DOI: 10.1111/gbi.12511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."
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Affiliation(s)
- Ana C Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tiantian Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- State Key Laboratory of Marine Environmental Science (Xiamen University), Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sarah Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | - Linda L Jahnke
- NASA Ames Research Center, Moffett Field, California, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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Degenhardt J, Merder J, Heyerhoff B, Simon H, Engelen B, Waska H. Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. Microorganisms 2021; 9:1720. [PMID: 34442799 PMCID: PMC8399146 DOI: 10.3390/microorganisms9081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.
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Affiliation(s)
- Julius Degenhardt
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Julian Merder
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Hannelore Waska
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
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Wang W, Tao J, Yu K, He C, Wang J, Li P, Chen H, Xu B, Shi Q, Zhang C. Vertical Stratification of Dissolved Organic Matter Linked to Distinct Microbial Communities in Subtropic Estuarine Sediments. Front Microbiol 2021; 12:697860. [PMID: 34354693 PMCID: PMC8329499 DOI: 10.3389/fmicb.2021.697860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022] Open
Abstract
Dissolved organic matter (DOM) provides carbon substrates and energy sources for sediment microbes driving benthic biogeochemical processes. The interactions between microbes and DOM are dynamic and complex and require the understanding based on fine-scale microbial community and physicochemical profiling. In this study, we characterized the porewater DOM composition in a 300-cm sediment core from the Pearl River estuary, China, and examined the interactions between DOM and archaeal and bacterial communities. DOM composition were highly stratified and associated with changing microbial communities. Compared to bacteria, the amplicon sequence variants of archaea showed significant Pearson correlations (r ≥ 0.65, P < 0.01) with DOM molecules of low H/C ratios, high C number and double bond equivalents, indicating that the distribution of archaea was closely correlated to recalcitrant DOM while bacteria were associated with relatively labile compounds. This was supported by the presence of auxiliary enzyme families essential for lignin degradation and bcrABCD, UbiX genes for anaerobic aromatic reduction in metagenome-assembled genomes of Bathyarchaeia. Our study demonstrates that niche differentiation between benthic bacteria and archaea may have important consequences in carbon metabolism, particularly for the transformation of recalcitrant organic carbon that may be predominant in aged marine sediments.
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Affiliation(s)
- Wenxiu Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jianchang Tao
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Penghui Li
- School of Marine Science, Sun Yat-sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Hongmei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Bu Xu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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10
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Suominen S, van Vliet DM, Sánchez-Andrea I, van der Meer MTJ, Sinninghe Damsté JS, Villanueva L. Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments. Front Microbiol 2021; 12:628301. [PMID: 34025597 PMCID: PMC8131844 DOI: 10.3389/fmicb.2021.628301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Daan M. van Vliet
- Wageningen Food and Biobased Research (WFBR), Bornse Weilanden 9, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | | | - Marcel T. J. van der Meer
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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Walker BD, Beaupré SR, Griffin S, Walker J, Druffel E, Xu X. A sealed-tube method for offline δ 13 C analysis of CO 2 via a Gas Bench II continuous-flow isotope ratio mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9040. [PMID: 33373477 DOI: 10.1002/rcm.9040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
RATIONALE The isotopic measurement of environmental sample CO2 via isotope ratio mass spectrometry (IRMS) can present many analytical challenges. In many offline applications, exceedingly few samples can be prepared per day. In such applications, long-term storage (months) of sample CO2 is desirable, in order to accumulate enough samples to warrant a day of isotopic measurements. Conversely, traditional sample tube cracker systems for dual-inlet IRMS offer a capacity for only 6-8 tubes and thus limit throughput. Here we present a simple method to alleviate these concerns using a Gas Bench II gas handling device coupled with continuous-flow IRMS. METHODS Sample preparation entails the cryogenic purification and quantification of CO2 on a vacuum line. Sample CO2 splits are expanded from a known volume to several sample ports and allowed to isotopically equilibrate (homogenize). Equilibrated CO2 splits are frozen into 3 mm outer diameter Pyrex break-seals and sealed under vacuum with a torch to a length of 5.5 cm. Sample break-seals are scored, placed into 12 mL Labco Exetainer® vials, purged with ultrahigh-purity helium, cracked inside the capped helium-flushed vials and subsequently measured via a Gas Bench equipped IRMS instrument using a CTC Analytics PAL autosampler. RESULTS Our δ13 C results from NIST and internal isotopic standards, measured over a time period of several years, indicate that the sealed-tube method produces accurate δ13 C values to a precision of ±0.1‰ for samples containing 10-35 μgC. The tube cracking technique within Exetainer vials has been optimized over a period of 10 years, resulting in decreased sample failure rates from 5-10% to <1%. CONCLUSIONS This technique offers an alternative method for δ13 C analyses of CO2 where offline isolation and long-term storage are desired. The method features a much higher sample throughput than traditional dual-inlet IRMS cracker setups at similar precision (±0.1‰).
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Affiliation(s)
- Brett D Walker
- Department of Earth and Environmental Sciences, University of Ottawa, Advanced Research Complex, 25 Templeton Street, Ottawa, Ontario, K1N 6N5, Canada
- Department of Earth System Science, University of California Irvine, 2212 Croul Hall, Irvine, CA, 92697-3100, USA
| | - Steven R Beaupré
- School of Marine and Atmospheric Sciences, 123 Challenger Hall, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Sheila Griffin
- Department of Earth System Science, University of California Irvine, 2212 Croul Hall, Irvine, CA, 92697-3100, USA
| | - Jennifer Walker
- Department of Earth and Environmental Sciences, University of Ottawa, Advanced Research Complex, 25 Templeton Street, Ottawa, Ontario, K1N 6N5, Canada
- Department of Earth System Science, University of California Irvine, 2212 Croul Hall, Irvine, CA, 92697-3100, USA
| | - Ellen Druffel
- Department of Earth System Science, University of California Irvine, 2212 Croul Hall, Irvine, CA, 92697-3100, USA
| | - Xiaomei Xu
- Department of Earth System Science, University of California Irvine, 2212 Croul Hall, Irvine, CA, 92697-3100, USA
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12
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Dai L, Liu C, Peng L, Song C, Li X, Tao L, Li G. Different distribution patterns of microorganisms between aquaculture pond sediment and water. J Microbiol 2021; 59:376-388. [PMID: 33630250 DOI: 10.1007/s12275-021-0635-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
Aquatic microorganisms in the sediment and water column are closely related; however, their distribution patterns between these two habitats still remain largely unknown. In this study, we compared sediment and water microeukaryotic and bacterial microorganisms in aquaculture ponds from different areas in China, and analyzed the influencing environmental factors as well as the inter-taxa relationships. We found that bacteria were significantly more abundant than fungi in both sediment and water, and the bacterial richness and diversity in sediment were higher than in water in all the sampling areas, but no significant differences were found between the two habitats for microeukaryotes. Bacterial taxa could be clearly separated through cluster analysis between the sediment and water, while eukaryotic taxa at all classification levels could not. Spirochaetea, Deltaproteobacteria, Nitrospirae, Ignavibacteriae, Firmicutes, Chloroflexi, and Lentimicrobiaceae were more abundantly distributed in sediment, while Betaproteobacteria, Alphaproteobacter, Cyanobacteria, Roseiflexaceae, Dinghuibacter, Cryomorphaceae, and Actinobacteria were more abundant in water samples. For eukaryotes, only Cryptomonadales were found to be distributed differently between the two habitats. Microorganisms in sediment were mainly correlated with enzymes related to organic matter decomposition, while water temperature, pH, dissolved oxygen, and nutrient levels all showed significant correlation with the microbial communities in pond water. Intensive interspecific relationships were also found among eukaryotes and bacteria. Together, our results indicated that eukaryotic microorganisms are distributed less differently between sediment and water in aquaculture ponds compared to bacteria. This study provides valuable data for evaluating microbial distributions in aquatic environments, which may also be of practical use in aquaculture pond management.
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Affiliation(s)
- Lili Dai
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
| | - Chengqing Liu
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
- College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, P. R. China
| | - Liang Peng
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
| | - Chaofeng Song
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
| | - Xiaoli Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
| | - Ling Tao
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China
| | - Gu Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 100141, P. R. China.
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13
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The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Root−associated microbial communities play important roles in the process of adaptation of plant hosts to environment stressors, and in this perspective, the microbiome of halophytes represents a valuable model for understanding the contribution of microorganisms to plant tolerance to salt. Although considered as the most promising halophyte candidate to crop cultivation, Salicornia ramosissima is one of the least-studied species in terms of microbiome composition and the effect of sediment properties on the diversity of plant-growth promoting bacteria associated with the roots. In this work, we aimed at isolating and characterizing halotolerant bacteria associated with the rhizosphere and root tissues of S. ramosissima, envisaging their application in saline agriculture. Endophytic and rhizosphere bacteria were isolated from wild and crop cultivated plants, growing in different estuarine conditions. Isolates were identified based on 16S rRNA sequences and screened for plant-growth promotion traits. The subsets of isolates from different sampling sites were very different in terms of composition but consistent in terms of the plant-growth promoting traits represented. Bacillus was the most represented genus and expressed the wider range of extracellular enzymatic activities. Halotolerant strains of Salinicola, Pseudomonas, Oceanobacillus, Halomonas, Providencia, Bacillus, Psychrobacter and Brevibacterium also exhibited several plant-growth promotion traits (e.g., 3-indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophores, phosphate solubilization). Considering the taxonomic diversity and the plant-growth promotion potential of the isolates, the collection represents a valuable resource that can be used to optimize the crop cultivation of Salicornia under different environmental conditions and for the attenuation of salt stress in non-halophytes, considering the global threat of arable soil salinization.
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14
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Zhang Y, Gan Y, Yu K, Han L. Fractionation of carbon isotopes of dissolved organic matter adsorbed to goethite in the presence of arsenic to study the origin of DOM in groundwater. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1225-1238. [PMID: 32651930 DOI: 10.1007/s10653-020-00644-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Natural dissolved organic matter (DOM) in groundwater plays a crucial role in mobilizing arsenic (As). The complex contribution of DOM sources makes it hard to predict how the variation of environmental conditions would affect the distribution of As concentrations. Identifying the carbon isotope fractionation of DOM is the key to quantify DOM sources based on stable carbon isotopes. To understand the magnitude and variability in the carbon isotopic fractionation of DOM in competitive adsorption with As(V), this study investigated the δ13C values of fulvic acid (FA) and DOM during adsorption to goethite in the presence of As(V), at a specific pH and temperature. The carbon isotopic enrichment factor (ε) of FA in the adsorption to goethite was 0.65 ± 2.11‰ at pH 4.1, 25 °C, suggesting that FA molecules containing 13C were more easily adsorbed to goethite. An increasing temperature increased εFA from 0.32 ± 1.17‰ to 0.82 ± 5.39‰ at 15-35 °C. For dissolved sediment organic matter (DSOM) cases, molecules containing 13C were more easily adsorbed to goethite. However, enrichment factors were not detected due to a reduction in DSOM adsorption and the diversity of natural humic substances or groups. The findings provide basic data for accurately ascertaining DOM sources through carbon isotopes, which is significant for predicting As fluctuation in aquifers affected by monsoon climate and/or human activities.
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Affiliation(s)
- Yanan Zhang
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, China
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan, 430074, China
| | - Yiqun Gan
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, China.
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan, 430074, China.
| | - Kai Yu
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, China
| | - Li Han
- School of Environment Studies, China University of Geosciences, Wuhan, 430074, China
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15
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Yang X, Chen S. Microorganisms in sediment microbial fuel cells: Ecological niche, microbial response, and environmental function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:144145. [PMID: 33303196 DOI: 10.1016/j.scitotenv.2020.144145] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
A sediment microbial fuel cell (SMFC) is a device that harvests electrical energy from sediments rich in organic matter. SMFCs have been attracting increasing amounts of interest in environmental remediation, since they are capable of providing a clean and inexhaustible source of electron donors or acceptors and can be easily controlled by adjusting the electrochemical parameters. The microorganisms inhabiting sediments and the overlying water play a pivotal role in SMFCs. Since the SMFC is applied in an open environment rather than in an enclosed chamber, the effects of the environment on the microbes should be intense and the microbial community succession should be extremely complex. Thus, this review aims to provide an overview of the microorganisms in SMFCs, which few previous review papers have reported. In this study, the anodic and cathodic niches for the microorganisms in SMFCs are summarized, how the microbial population and community interact with the SMFC environment is discussed, a new microbial succession strategy called the electrode stimulation succession is proposed, and recent developments in the environmental functions of SMFCs are discussed from the perspective of microorganisms. Future studies are needed to investigate the electrode stimulation succession, the environmental function and the electron transfer mechanism in order to boost the application of SMFCs for power generation and environmental remediation.
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Affiliation(s)
- Xunan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Shanshan Chen
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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16
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Stern RA, Mahmoudi N, Buckee CO, Schartup AT, Koutrakis P, Ferguson ST, Wolfson JM, Wofsy SC, Daube BC, Sunderland EM. The Microbiome of Size-Fractionated Airborne Particles from the Sahara Region. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1487-1496. [PMID: 33474936 DOI: 10.1021/acs.est.0c06332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Diverse airborne microbes affect human health and biodiversity, and the Sahara region of West Africa is a globally important source region for atmospheric dust. We collected size-fractionated (>10, 10-2.5, 2.5-1.0, 1.0-0.5, and <0.5 μm) atmospheric particles in Mali, West Africa and conducted the first cultivation-independent study of airborne microbes in this region using 16S rRNA gene sequencing. Abundant and diverse microbes were detected in all particle size fractions at levels higher than those previously hypothesized for desert regions. Average daily abundance was 1.94 × 105 16S rRNA copies/m3. Daily patterns in abundance for particles <0.5 μm differed significantly from other size fractions likely because they form mainly in the atmosphere and have limited surface resuspension. Particles >10 μm contained the greatest fraction of daily abundance (51-62%) and had significantly greater diversity than smaller particles. Greater bacterial abundance of particles >2.5 μm that are bigger than the average bacterium suggests that most airborne bacteria are present as aggregates or attached to particles rather than as free-floating cells. Particles >10 μm have very short atmospheric lifetimes and thus tend to have more localized origins. We confirmed the presence of several potential pathogens using polymerase chain reaction that are candidates for viability and strain testing in future studies. These species were detected on all particle sizes tested, including particles <2.5 μm that are expected to undergo long-range transport. Overall, our results suggest that the composition and sources of airborne microbes can be better discriminated by collecting size-fractionated samples.
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Affiliation(s)
- Rebecca A Stern
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montreal, Quebec H3A 0E8, Canada
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Amina T Schartup
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Petros Koutrakis
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Stephen T Ferguson
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Jack M Wolfson
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Steven C Wofsy
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bruce C Daube
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Elsie M Sunderland
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
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17
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Samuels T, Bryce C, Landenmark H, Marie‐Loudon C, Nicholson N, Stevens AH, Cockell C. Microbial Weathering of Minerals and Rocks in Natural Environments. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/9781119413332.ch3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Mahmoudi N, Enke TN, Beaupré SR, Teske AP, Cordero OX, Pearson A. Illuminating microbial species‐specific effects on organic matter remineralization in marine sediments. Environ Microbiol 2019; 22:1734-1747. [DOI: 10.1111/1462-2920.14871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/15/2019] [Accepted: 11/19/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Nagissa Mahmoudi
- Department of Earth and Planetary Sciences McGill University Montreal QC H3A 0E8
| | - Tim N. Enke
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Steven R. Beaupré
- School of Marine and Atmospheric Sciences Stony Brook University Stony Brook New York 11794
| | - Andreas P. Teske
- Department of Marine Sciences University of North Carolina Chapel Hill North Carolina 27599
| | - Otto X. Cordero
- Department of Civil and Environmental Engineering Massachusetts Institute of Technology (MIT) Cambridge Massachusetts 02139
| | - Ann Pearson
- Department of Earth and Planetary Sciences Harvard University Cambridge Massachusetts 02138
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19
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D'Hondt S, Pockalny R, Fulfer VM, Spivack AJ. Subseafloor life and its biogeochemical impacts. Nat Commun 2019; 10:3519. [PMID: 31388058 PMCID: PMC6684631 DOI: 10.1038/s41467-019-11450-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 07/10/2019] [Indexed: 11/08/2022] Open
Abstract
Subseafloor microbial activities are central to Earth's biogeochemical cycles. They control Earth's surface oxidation and major aspects of ocean chemistry. They affect climate on long timescales and play major roles in forming and destroying economic resources. In this review, we evaluate present understanding of subseafloor microbes and their activities, identify research gaps, and recommend approaches to filling those gaps. Our synthesis suggests that chemical diffusion rates and reaction affinities play a primary role in controlling rates of subseafloor activities. Fundamental aspects of subseafloor communities, including features that enable their persistence at low catabolic rates for millions of years, remain unknown.
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Affiliation(s)
- Steven D'Hondt
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA.
| | - Robert Pockalny
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Victoria M Fulfer
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
| | - Arthur J Spivack
- Graduate School of Oceanography, University of Rhode Island Narragansett Bay Campus, 215 South Ferry Road, Rhode Island, 02882, USA
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20
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Miao L, Wang P, Hou J, Yao Y, Liu Z, Liu S. Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:705-713. [PMID: 30759596 DOI: 10.1016/j.scitotenv.2018.10.354] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
In this study, we investigated the effects of copper oxide (CuO) NPs on freshwater sediment biofilms in terms of the functional properties and microbial community structure. Biofilms were incubated in microcosms and CuO NPs (1 mg/L uncoated and humic-acid-coated) were exposed with Cu2+ (Cu(NO3)2) as the positive control. As determined from DO (dissolved oxygen) microelectrodes measurements, a high-DO region emerged inside the biofilms after 5-day exposure to CuO NPs compared with those before NP additions, which suggested CuO NPs inhibit the oxygen respiration activity. These results were consistent with the decreased heterotrophic respiration. CuO NPs significantly altered the bacterial community composition and decreased the abundances of Anaerolineaceae, Acidobacteria, Aminicenantes, and Anaerolinea. Functional analysis from PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)-predicted metagenomes indicated that bacterial genera depleted by CuO NP treatments were related to carbohydrate and glycan biosynthesis and metabolism, and biosynthesis of other secondary metabolites. These functional profiles combined with the decreased activities of extracellular enzymes, β-glucosidase (GLU) and l-leucine aminopeptidase (LAP), suggested that the introduction of CuO NPs exhibit negative effects on the biogeochemical processes and the cycling of carbon and nitrogen in biofilm systems. Whereas these toxic effects of CuO NPs could be mitigated when the aquatic environment is enriched with natural organic matters such as humic acid.
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Affiliation(s)
- Lingzhan Miao
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Peifang Wang
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Jun Hou
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China.
| | - Yu Yao
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Zhilin Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
| | - Songqi Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, People's Republic of China
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21
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Dynamics of phosphorus and bacterial phoX genes during the decomposition of Microcystis blooms in a mesocosm. PLoS One 2018; 13:e0195205. [PMID: 29723219 PMCID: PMC5933731 DOI: 10.1371/journal.pone.0195205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial blooms are a worldwide environmental problem and frequently occur in eutrophic lakes. Organophosphorus mineralization regulated by microbial alkaline phosphatase provides available nutrients for bloom regeneration. To uncover the dynamics of bacterial alkaline phosphatase activity and microbial backgrounds in relation to organophosphorus mineralization during the decomposition process of cyanobacterial blooms, the response of alkaline phosphatase PhoX-producing bacteria were explored using a 23-day mesocosm experiment with three varying densities of Microcystis biomass from eutrophic Lake Taihu. Our study found large amounts of soluble reactive phosphorus and dissolved organophosphorus were released into the lake water during the decomposition process. Bacterial alkaline phosphatase activity showed the peak values during days 5~7 in groups with different chlorophyll-a densities, and then all decreased dramatically to their initial experimental levels during the last stage of decomposition. Bacterial phoX abundances in the three experimental groups increased significantly along with the decomposition process, positively related to the dissolved organic carbon and organophosphorus released by the Microcystis blooms. The genotypes similar to the phoX genes of Alphaproteobacteria were dominant in all groups, whereas the genotypes most similar to the phoX genes of Betaproteobacteria and Cyanobacteria were also abundant in the low density (~15 μg L-1 chlorophyll-a) group. At the end of the decomposition process, the number of genotypes most similar to the phoX of Betaproteobacteria and Cyanobacteria increased in the medium (~150 μg L-1 chlorophyll-a) and high (~1500 μg L-1 chlorophyll-a) density groups. The released organophosphorus and increased bacterial phoX abundance after decomposition of Microcystis aggregates could potentially provide sufficient nutrients and biological conditions for algal proliferation and are probably related to the regeneration of Microcystis blooms in eutrophic lakes.
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22
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Mullen L, Boerrigter K, Ferriero N, Rosalsky J, Barrett AVB, Murray PJ, Steen AD. Potential Activities of Freshwater Exo- and Endo-Acting Extracellular Peptidases in East Tennessee and the Pocono Mountains. Front Microbiol 2018; 9:368. [PMID: 29559961 PMCID: PMC5845674 DOI: 10.3389/fmicb.2018.00368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/16/2018] [Indexed: 11/29/2022] Open
Abstract
Proteins constitute a particularly bioavailable subset of organic carbon and nitrogen in aquatic environments but must be hydrolyzed by extracellular enzymes prior to being metabolized by microorganisms. Activities of extracellular peptidases (protein-degrading enzymes) have frequently been assayed in freshwater systems, but such studies have been limited to substrates for a single enzyme [leucyl aminopeptidase (Leu-AP)] out of more than 300 biochemically recognized peptidases. Here, we report kinetic measurements of extracellular hydrolysis of five substrates in 28 freshwater bodies in the Delaware Water Gap National Recreation Area in the Pocono Mountains (PA, United States) and near Knoxville (TN, United States), between 2013 and 2016. The assays putatively test for four aminopeptidases (arginyl aminopeptidase, glyclyl aminopeptidase, Leu-AP, and pyroglutamyl aminopeptidase), which cleave N-terminal amino acids from proteins, and trypsin, an endopeptidase, which cleaves proteins mid-chain. Aminopeptidase and the trypsin-like activity were observed in all water bodies, indicating that a diverse set of peptidases is typical in freshwater. However, ratios of peptidase activities were variable among sites: aminopeptidases dominated at some sites and trypsin-like activity at others. At a given site, the ratios remained fairly consistent over time, indicating that they are driven by ecological factors. Studies in which only Leu-AP activity is measured may underestimate the total peptidolytic capacity of an environment, due to the variable contribution of endopeptidases.
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Affiliation(s)
- Lauren Mullen
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Kim Boerrigter
- Malcolm X Shabazz High School, Newark, NJ, United States.,Harvard College, Cambridge, MA, United States
| | | | - Jeff Rosalsky
- Pocono Environmental Education Center, Dingmans Ferry, PA, United States
| | - Abigail van Buren Barrett
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Andrew D Steen
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
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23
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Valle J, Gonsior M, Harir M, Enrich-Prast A, Schmitt-Kopplin P, Bastviken D, Conrad R, Hertkorn N. Extensive processing of sediment pore water dissolved organic matter during anoxic incubation as observed by high-field mass spectrometry (FTICR-MS). WATER RESEARCH 2018; 129:252-263. [PMID: 29153878 DOI: 10.1016/j.watres.2017.11.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/14/2017] [Accepted: 11/05/2017] [Indexed: 06/07/2023]
Abstract
Dissolved organic matter (DOM) contained in lake sediments is a carbon source for many microbial degradation processes, including aerobic and anaerobic mineralization. During anaerobic degradation, DOM is partially consumed and transformed into new molecules while the greenhouse gases methane (CH4) and carbon dioxide (CO2) are produced. In this study, we used ultrahigh resolution mass spectrometry to trace differences in the composition of solid-phase extractable (PPL resin) pore water DOM (SPE-DOM) isolated from surface sediments of three boreal lakes before and after 40 days of anoxic incubation, with concomitant determination of CH4 and CO2 evolution. CH4 and CO2 production detected by gas chromatography varied considerably among replicates and accounted for fractions of ∼2-4 × 10-4 of sedimentary organic carbon for CO2 and ∼0.8-2.4 × 10-5 for CH4. In contrast, the relative changes of key bulk parameters during incubation, such as relative proportions of molecular series, elemental ratios, average mass and unsaturation, were regularly in the percent range (1-3% for compounds decreasing and 4-10% for compounds increasing), i.e. several orders of magnitude higher than mineralization alone. Computation of the average carbon oxidation state in CHO molecules of lake pore water DOM revealed rather non-selective large scale transformations of organic matter during incubation, with depletion of highly oxidized and highly reduced CHO molecules, and formation of rather non-labile fulvic acid type molecules. In general, proportions of CHO compounds slightly decreased. Nearly saturated CHO and CHOS lipid-like substances declined during incubation: these rather commonplace molecules were less specific indicators of lake sediment alteration than the particular compounds, such as certain oxygenated aromatics and carboxyl-rich alicyclic acids (CRAM) found more abundant after incubation. There was a remarkable general increase in many CHNO compounds during incubation across all lakes. Differences in DOM transformation between lakes corresponded with lake size and water residence time. While in the small lake Svarttjärn, CRAM increased during incubation, lignin-and tannin-like compounds were enriched in the large lake Bisen, suggesting selective preservation of these rather non-labile aromatic compounds rather than recent synthesis. SPE-DOM after incubation may represent freshly synthesized compounds, leftover bulk DOM which is primarily composed of intrinsically refractory molecules and/or microbial metabolites which were not consumed in our experiments. In spite of a low fraction of the total DOM being mineralized to CO2 and CH4, the more pronounced change in molecular DOM composition during the incubation indicates that diagenetic modification of organic matter can be substantial compared to complete mineralization.
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Affiliation(s)
- Juliana Valle
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Gonsior
- University of Maryland Center for Environmental Science, Chesapeake Biological Laboratory, Solomons, USA
| | - Mourad Harir
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany; Department for Chemical-Technical Analysis, Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - Alex Enrich-Prast
- Linköping University, Department of Thematic Studies-Environmental Change, Linköping, Sweden; Federal University of Rio de Janeiro, Department of Botany, Rio de Janeiro, Brazil.
| | - Philippe Schmitt-Kopplin
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany; Department for Chemical-Technical Analysis, Research Center Weihenstephan for Brewing and Food Quality, Technische Universität München, Freising-Weihenstephan, Germany
| | - David Bastviken
- Linköping University, Department of Thematic Studies-Environmental Change, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Norbert Hertkorn
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany.
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