1
|
Schiksnis C, Xu M, Saito MA, McIlvin M, Moran D, Bian X, John SG, Zheng Q, Yang N, Fu F, Hutchins DA. Proteomics analysis reveals differential acclimation of coastal and oceanic Synechococcus to climate warming and iron limitation. Front Microbiol 2024; 15:1323499. [PMID: 38444803 PMCID: PMC10912551 DOI: 10.3389/fmicb.2024.1323499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/30/2024] [Indexed: 03/07/2024] Open
Abstract
In many oceanic regions, anthropogenic warming will coincide with iron (Fe) limitation. Interactive effects between warming and Fe limitation on phytoplankton physiology and biochemical function are likely, as temperature and Fe availability affect many of the same essential cellular pathways. However, we lack a clear understanding of how globally significant phytoplankton such as the picocyanobacteria Synechococcus will respond to these co-occurring stressors, and what underlying molecular mechanisms will drive this response. Moreover, ecotype-specific adaptations can lead to nuanced differences in responses between strains. In this study, Synechococcus isolates YX04-1 (oceanic) and XM-24 (coastal) from the South China Sea were acclimated to Fe limitation at two temperatures, and their physiological and proteomic responses were compared. Both strains exhibited reduced growth due to warming and Fe limitation. However, coastal XM-24 maintained relatively higher growth rates in response to warming under replete Fe, while its growth was notably more compromised under Fe limitation at both temperatures compared with YX04-1. In response to concurrent heat and Fe stress, oceanic YX04-1 was better able to adjust its photosynthetic proteins and minimize the generation of reactive oxygen species while reducing proteome Fe demand. Its intricate proteomic response likely enabled oceanic YX04-1 to mitigate some of the negative impact of warming on its growth during Fe limitation. Our study highlights how ecologically-shaped adaptations in Synechococcus strains even from proximate oceanic regions can lead to differing physiological and proteomic responses to these climate stressors.
Collapse
Affiliation(s)
- Cara Schiksnis
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Min Xu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Matthew McIlvin
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Dawn Moran
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Xiaopeng Bian
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Seth G. John
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nina Yang
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
- Marine Policy Center, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Feixue Fu
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| | - David A. Hutchins
- Marine and Environmental Biology, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
2
|
Goldman AL, Fulk EM, Momper LM, Heider C, Mulligan J, Osburn M, Masiello CA, Silberg JJ. Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface. mSystems 2024; 9:e0096623. [PMID: 38059636 PMCID: PMC10805038 DOI: 10.1128/msystems.00966-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
Microbes can be found in abundance many kilometers underground. While microbial metabolic capabilities have been examined across different geochemical settings, it remains unclear how changes in subsurface niches affect microbial needs to sense and respond to their environment. To address this question, we examined how microbial extracellular sensor systems vary with environmental conditions across metagenomes at different Deep Mine Microbial Observatory (DeMMO) subsurface sites. Because two-component systems (TCSs) directly sense extracellular conditions and convert this information into intracellular biochemical responses, we expected that this sensor family would vary across isolated oligotrophic subterranean environments that differ in abiotic and biotic conditions. TCSs were found at all six subsurface sites, the service water control, and the surface site, with an average of 0.88 sensor histidine kinases (HKs) per 100 genes across all sites. Abundance was greater in subsurface fracture fluids compared with surface-derived fluids, and candidate phyla radiation (CPR) bacteria presented the lowest HK frequencies. Measures of microbial diversity, such as the Shannon diversity index, revealed that HK abundance is inversely correlated with microbial diversity (r2 = 0.81). Among the geochemical parameters measured, HK frequency correlated most strongly with variance in dissolved organic carbon (r2 = 0.82). Taken together, these results implicate the abiotic and biotic properties of an ecological niche as drivers of sensor needs, and they suggest that microbes in environments with large fluctuations in organic nutrients (e.g., lacustrine, terrestrial, and coastal ecosystems) may require greater TCS diversity than ecosystems with low nutrients (e.g., open ocean).IMPORTANCEThe ability to detect extracellular environmental conditions is a fundamental property of all life forms. Because microbial two-component sensor systems convert information about extracellular conditions into biochemical information that controls their behaviors, we evaluated how two-component sensor systems evolved within the deep Earth across multiple sites where abiotic and biotic properties vary. We show that these sensor systems remain abundant in microbial consortia at all subterranean sampling sites and observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties. These results suggest that multiple environmental properties may drive sensor protein evolution and highlight the need for further studies of metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.
Collapse
Affiliation(s)
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Lily M. Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Clinton Heider
- Rice University, Center for Research Computing, Houston, Texas, USA
| | - John Mulligan
- Rice University, Center for Research Computing, Houston, Texas, USA
| | - Magdalena Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Caroline A. Masiello
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, Texas, USA
- Department of Chemistry, Rice University, Houston, Texas, USA
| | - Jonathan J. Silberg
- Department of Biosciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| |
Collapse
|
3
|
Jackrel SL, White JD, Perez-Coronel E, Koch RY. Selection for oligotrophy among bacteria inhabiting host microbiomes. mBio 2023; 14:e0141523. [PMID: 37646528 PMCID: PMC10653850 DOI: 10.1128/mbio.01415-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/04/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.
Collapse
Affiliation(s)
- Sara L. Jackrel
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Jeffrey D. White
- Department of Biology, Framingham State University, Framingham, Massachusetts, USA
| | - Elisabet Perez-Coronel
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| | - Ryan Y. Koch
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
4
|
Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
Collapse
Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | |
Collapse
|
5
|
Noell SE, Brennan E, Washburn Q, Davis EW, Hellweger FL, Giovannoni SJ. Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility. Environ Microbiol 2023. [PMID: 36826469 DOI: 10.1111/1462-2920.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/22/2023] [Indexed: 02/25/2023]
Abstract
Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14 C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
Collapse
Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Elizabeth Brennan
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Edward W Davis
- Center for Quantitative Life Sciences, Oregon State University, Oregon, USA
| | | | | |
Collapse
|
6
|
Yang N, Lin YA, Merkel CA, DeMers MA, Qu PP, Webb EA, Fu FX, Hutchins DA. Molecular mechanisms underlying iron and phosphorus co-limitation responses in the nitrogen-fixing cyanobacterium Crocosphaera. THE ISME JOURNAL 2022; 16:2702-2711. [PMID: 36008474 PMCID: PMC9666452 DOI: 10.1038/s41396-022-01307-7] [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: 02/27/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
In the nitrogen-limited subtropical gyres, diazotrophic cyanobacteria, including Crocosphaera, provide an essential ecosystem service by converting dinitrogen (N2) gas into ammonia to support primary production in these oligotrophic regimes. Natural gradients of phosphorus (P) and iron (Fe) availability in the low-latitude oceans constrain the biogeography and activity of diazotrophs with important implications for marine biogeochemical cycling. Much remains unknown regarding Crocosphaera's physiological and molecular responses to multiple nutrient limitations. We cultured C. watsonii under Fe, P, and Fe/P (co)-limiting scenarios to link cellular physiology with diel gene expression and observed unique physiological and transcriptional profiles for each treatment. Counterintuitively, reduced growth and N2 fixation resource use efficiencies (RUEs) for Fe or P under P limitation were alleviated under Fe/P co-limitation. Differential gene expression analyses show that Fe/P co-limited cells employ the same responses as single-nutrient limited cells that reduce cellular nutrient requirements and increase responsiveness to environmental change including smaller cell size, protein turnover (Fe-limited), and upregulation of environmental sense-and-respond systems (P-limited). Combined, these mechanisms enhance growth and RUEs in Fe/P co-limited cells. These findings are important to our understanding of nutrient controls on N2 fixation and the implications for primary productivity and microbial dynamics in a changing ocean.
Collapse
Affiliation(s)
- Nina Yang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yu-An Lin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Carlin A Merkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Michelle A DeMers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ping-Ping Qu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fei-Xue Fu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Hutchins
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
7
|
Wei SS, Yen CM, Marshall IPG, Hamid HA, Kamal SS, Nielsen DS, Ahmad HF. Gut microbiome and metabolome of sea cucumber (Stichopus ocellatus) as putative markers for monitoring the marine sediment pollution in Pahang, Malaysia. MARINE POLLUTION BULLETIN 2022; 182:114022. [PMID: 35963228 DOI: 10.1016/j.marpolbul.2022.114022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic contamination in the marine environment forms an emerging threat to marine ecosystems. This study aimed to compare the gut and coelomic microbiota of Stichopus ocellatus with sediments between two coastal districts of Pahang, which potentially conferring as putative biomarkers for sediment pollution monitoring. The composition of the bacteria communities was determined using 16S rRNA V3-region gene amplicon sequencing, while hybrid whole-genome sequencing was employed to analyze the genome of Vibrio parahaemolyticus. The trace elements and antibiotic compositions were access using high-throughput spectrometry. The alpha- and beta-diversity of bacteria in gut and sediment samples from Kuantan differed substantially within (p-value = 0.017604) and between samples (p-value <0.007), respectively. Vibrio genera predominated in Kuantan samples, while Flavobacterium and Synechococcus_E genera predominated in Pekan samples. Vibrio parahaemolyticus revealed the presence of tet(35) and blaCARB-33 genes that conceived resistance towards tetracycline and beta-lactam antibiotics, respectively, which were detected in sediment and gut samples.
Collapse
Affiliation(s)
- Siew Shing Wei
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Choo Mei Yen
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia
| | - Ian P G Marshall
- Center for Electromicrobiology, Department of Biology, Ny Munkegade 116, 8000 Aarhus C, Denmark.
| | - Hazrulrizawati Abd Hamid
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia; Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia.
| | - Shamrulazhar Shamzir Kamal
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
| | | | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences & Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Pahang, Malaysia.
| |
Collapse
|
8
|
Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column. mBio 2022; 13:e0156922. [PMID: 35862780 PMCID: PMC9426571 DOI: 10.1128/mbio.01569-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean.
Collapse
|
9
|
Zhao Y, Min H, Luo K, Zhang R, Chen Q, Chen Z. Transcriptomics and proteomics revealed the psychrotolerant and antibiotic-resistant mechanisms of strain Pseudomonas psychrophila RNC-1 capable of assimilatory nitrate reduction and aerobic denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153169. [PMID: 35051480 DOI: 10.1016/j.scitotenv.2022.153169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Aerobic denitrification has been proved to be profoundly affected by temperature and antibiotics, but little is known about how aerobic denitrifiers respond to temperature and antibiotic stress. In this study, the nitrate reduction performance and the intracellular metabolism by a psychrotolerant aerobic denitrifying bacteria, named Pseudomonas psychrophila RNC-1, were systematically investigated at different temperatures (10 °C, 20 °C, 30 °C) and different sulfamethoxazole (SMX) concentrations (0 mg/L, 0.1 mg/L, 0.5 mg/L, 1.0 mg/L, and 5.0 mg/L). The results showed that strain RNC-1 performed satisfactory nitrate removal at 10 °C and 20 °C, but its growth was significantly inhibited at 30 °C. Nitrate removal by strain RNC-1 was slightly promoted in the presence of 0.5 mg/L SMX, whereas it was significantly suppressed with 5.0 mg/L SMX. Nitrogen balance analysis indicated that assimilatory nitrate reduction and dissimilatory aerobic denitrification jointly dominated in the nitrate removal process of strain RNC-1, in which the inhibition effected on assimilation process was much higher than that on the aerobic denitrification process under SMX exposure. Further transcriptomics and proteomics analysis revealed that the psychrotolerant mechanism of strain RNC-1 could be attributed to the up-regulation of RNA translation, energy metabolism, ABC transporters and the over-expression of cold shock proteins, while the down-regulation of oxidative phosphorylation pathway was the primary reason for the deteriorative cell growth at 30 °C. The promotion of nitrate reduction with 0.5 mg/L SMX was related to the up-regulation of amino acid metabolism pathways, while the down-regulation of folate cycle, glycolysis/gluconeogenesis and bacterial chemotaxis pathways were responsible for the inhibition effect at 5.0 mg/L SMX. This work provides a mechanistic understanding of the metabolic adaption of strain RNC-1 under different stress, which is of significance for its application in nitrogen contaminated wastewater treatment processes.
Collapse
Affiliation(s)
- Yuanyi Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Hongchao Min
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China
| | - Kongyan Luo
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China
| | - Ruijie Zhang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, PR China; State Environmental Protection Key Laboratory of All Materials Flux in River Ecosystems, Beijing 100871, PR China.
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, PR China.
| |
Collapse
|
10
|
Zhao L, Brugel S, Ramasamy KP, Andersson A. Response of Coastal Shewanella and Duganella Bacteria to Planktonic and Terrestrial Food Substrates. Front Microbiol 2022; 12:726844. [PMID: 35250896 PMCID: PMC8888917 DOI: 10.3389/fmicb.2021.726844] [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: 06/17/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∼1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.
Collapse
Affiliation(s)
- Li Zhao
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Sonia Brugel
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Kesava Priyan Ramasamy
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
- Umeå Marine Sciences Centre, Umeå University, Hörnefors, Sweden
| |
Collapse
|
11
|
Rapp JZ, Sullivan MB, Deming JW. Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol 2021; 12:701186. [PMID: 34367102 PMCID: PMC8339730 DOI: 10.3389/fmicb.2021.701186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.
Collapse
Affiliation(s)
- Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States.,Department of Microbiology, Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States.,Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
| |
Collapse
|
12
|
Held NA, Sutherland KM, Webb EA, McIlvin MR, Cohen NR, Devaux AJ, Hutchins DA, Waterbury JB, Hansel CM, Saito MA. Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics. ISME COMMUNICATIONS 2021; 1:35. [PMID: 36739337 PMCID: PMC9723768 DOI: 10.1038/s43705-021-00034-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle-colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium's ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.
Collapse
Affiliation(s)
- Noelle A Held
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Kevin M Sutherland
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - Eric A Webb
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Matthew R McIlvin
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Natalie R Cohen
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Alexander J Devaux
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - John B Waterbury
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| |
Collapse
|
13
|
Rathour R, Gupta J, Mishra A, Rajeev AC, Dupont CL, Thakur IS. A comparative metagenomic study reveals microbial diversity and their role in the biogeochemical cycling of Pangong lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139074. [PMID: 32417476 DOI: 10.1016/j.scitotenv.2020.139074] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 05/20/2023]
Abstract
The environment of a high altitude brackish water lake presents an unprecedented reservoir for the microbial community with adaptability towards surviving stressful conditions. Pangong lake is a high altitude brackish water lake of the Himalayas situated in the eastern part of Ladakh (Indian Tibet), at the height of 4250 m above the sea level. Shotgun metagenomics sequencing of Pangong Lake sediments was performed to examine the taxonomic diversity and functional adaptations of the resident psychrophilic and psychrotolerant microbial communities of the lake (September; a temperature of ±10 °C). Proteobacteria was the most prominent phylum, and Methylophaga, Halomonas, and Marinobacter were mainly abundant at the genus level. Enzyme pathways responsible for methane metabolism, nitrogen metabolism, sulfur reduction, benzoate, and xylene degradation appeared to be complete in the metagenomic dataset. Stress response genes responsible for adaption to pH, cold, salt tolerance, osmotic stress, and oxidative stress were also found in abundance in the metagenome. We compared the Pangong lake metagenome sample to sediments and water samples from three different aquatic habitats, namely saline lake, freshwater lakes and marine ecosystem using MG-RAST server against RefSeq and Subsystem databases. The Pangong lake microbial community contains six unique genera. Regression analysis using metagenome samples suggested that Pangong lake was most closely related to the Trophic South Pacific Ocean (R2 = 0.971) and Socompa lake ecosystem (R2 = 0.991) at phylum and functional level II, respectively. Our study signifies that the functional metabolic potentiality of Pangong lake is strongly influenced by the taxonomic structure and environmental conditions. We are reporting the metagenome of the sediment sample of the Pangong lake, which unveils the microbial diversity and their functional potential.
Collapse
Affiliation(s)
- Rashmi Rathour
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India; J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Arti Mishra
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Aparna C Rajeev
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | | | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
| |
Collapse
|
14
|
Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. MICROBIAL ECOLOGY 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
Collapse
Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| |
Collapse
|
15
|
Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus. Proc Natl Acad Sci U S A 2020; 117:15740-15747. [PMID: 32576688 DOI: 10.1073/pnas.2001393117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.
Collapse
|
16
|
Zou Y, Yan J, Hou S, Yi Y, Cui B. Intensive land uses modify assembly process and potential metabolic function of edaphic bacterial communities in the Yellow River Delta, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 720:137713. [PMID: 32325607 DOI: 10.1016/j.scitotenv.2020.137713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Coastal reclamation is a global threat to natural ecosystems, disturbing biological community structure, diversity and ecological function through habitat conversion. We have limited insights into the changes brought about by coastal reclamation for different land-use types. We used the Yellow River Delta (YRD) as a model because it is a region with intensive land reclamation, and we investigated the structural and functional variations of bacterial communities and their relations to edaphic properties under different land-use types. Our results showed that the high soil organic carbon (SOC), nitrate concentrations and salinity were found in oil field, aquaculture pond and salt pan, respectively, and low values in natural wetland. Land use was found to have significant influence on bacterial community diversity. To investigate the phylogenetic conservation of specific traits, we analyzed the relationship between soil bacterial assembly processes and edaphic properties. Bacterial traits phylogenetically conserved, and differs in depth. Our findings suggest that SOC served as a deep trait due to it negative correlation with deeper branches of phylogenetic clustering, while nitrate functioned as a shallow trait due to its positive correlation with phylogenetic clustering at finer branches. Soil salinity acted as a complex trait effected on both finer and deeper branches. Further potential functional gene co-occurrence network analysis revealed that land reclamation induced shifts of metabolic function by altering the functional gene connectivity. We found that the photosynthesis pathway was enriched in hub modules related to oil field (OF), while methane metabolism was enriched in hub modules linked to sea cucumber pond (CP1). In addition, two-component systems (TCS) were enriched with nitrate, ammonia, SOC and salinity-related modules. Therefore, our study highlights the importance of integrating multi-function and multi-process identification and prediction of coastal diverse reclamation impacts on coastal ecosystems.
Collapse
Affiliation(s)
- Yuxuan Zou
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Jiaguo Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yujun Yi
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China
| | - Baoshan Cui
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, 100875 Beijing, China.
| |
Collapse
|
17
|
Mazzotta MG, McIlvin MR, Saito MA. Characterization of the Fe metalloproteome of a ubiquitous marine heterotroph, Pseudoalteromonas (BB2-AT2): multiple bacterioferritin copies enable significant Fe storage. Metallomics 2020; 12:654-667. [PMID: 32301469 PMCID: PMC8161647 DOI: 10.1039/d0mt00034e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fe is a critical nutrient to the marine biological pump, which is the process that exports photosynthetically fixed carbon in the upper ocean to the deep ocean. Fe limitation controls photosynthetic activity in major regions of the oceans, and the subsequent degradation of exported photosynthetic material is facilitated particularly by marine heterotrophic bacteria. Despite their importance in the carbon cycle and the scarcity of Fe in seawater, the Fe requirements, storage and cytosolic utilization of these marine heterotrophs has been less studied. Here, we characterized the Fe metallome of Pseudoalteromonas (BB2-AT2). We found that with two copies of bacterioferritin (Bfr), Pseudoalteromonas possesses substantial capacity for luxury uptake of Fe. Fe : C in the whole cell metallome was estimated (assuming C : P stoichiometry ∼51 : 1) to be between ∼83 μmol : mol Fe : C, ∼11 fold higher than prior marine bacteria surveys. Under these replete conditions, other major cytosolic Fe-associated proteins were observed including superoxide dismutase (SodA; with other metal SOD isoforms absent under Fe replete conditions) and catalase (KatG) involved in reactive oxygen stress mitigation and aconitase (AcnB), succinate dehydrogenase (FrdB) and cytochromes (QcrA and Cyt1) involved in respiration. With the aid of singular value decomposition (SVD), we were able to computationally attribute peaks within the metallome to specific metalloprotein contributors. A putative Fe complex TonB transporter associated with the closely related Alteromonas bacterium was found to be abundant within the Pacific Ocean mesopelagic environment. Despite the extreme scarcity of Fe in seawater, the marine heterotroph Pseudoalteromonas has expansive Fe storage capacity and utilization strategies, implying that within detritus and sinking particles environments, there is significant opportunity for Fe acquisition. Together these results imply an evolved dedication of marine Pseudoalteromonas to maintaining an Fe metalloproteome, likely due to its dependence on Fe-based respiratory metabolism.
Collapse
Affiliation(s)
- Michael G Mazzotta
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA.
| | | | | |
Collapse
|
18
|
Tran HT, Wang HC, Hsu TW, Sarkar R, Huang CL, Chiang TY. Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes. BMC Genomics 2019; 20:478. [PMID: 31185914 PMCID: PMC6558789 DOI: 10.1186/s12864-019-5875-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan. Results In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers. Conclusions The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria. Electronic supplementary material The online version of this article (10.1186/s12864-019-5875-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Huyen-Trang Tran
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.,Department of Biology, Institute of Natural Science Education, Vinh University, Vinh, Nghe An, 461010, Vietnam
| | - Hao-Chu Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, Nantou, Taiwan, 55244
| | - Rakesh Sarkar
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.
| |
Collapse
|