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Herfort L, Crump BC, Fortunato CS, McCue LA, Campbell V, Simon HM, Baptista AM, Zuber P. Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima. Microbiologyopen 2017; 6. [PMID: 28782284 PMCID: PMC5727365 DOI: 10.1002/mbo3.522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/15/2017] [Accepted: 06/23/2017] [Indexed: 11/30/2022] Open
Abstract
Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production (3H‐leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1–24 PSU), but summer non‐ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free‐living (0.2–3 μm) assemblages of non‐ETM waters were similar to each other, indicating that particle‐attached (>3 μm) non‐ETM bacteria do not develop a distinct community. Brackish water type (ETM or non‐ETM) is thus a major factor affecting particle‐attached bacterial communities. Heterotrophic production was higher in particle‐attached than free‐living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM‐impacted waters). However, free‐living communities showed higher productivity prior to or after an ETM event (i.e., non‐ETM‐impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the existence of three particle types characterized by different bacterial communities in ETM, ETM‐impacted, and non‐ETM‐impacted brackish waters. Taxonomic analysis suggests that ETM key biological function is to remineralize organic matter.
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Affiliation(s)
- Lydie Herfort
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - Byron C Crump
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Caroline S Fortunato
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, USA
| | - Lee Ann McCue
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Victoria Campbell
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA
| | - Holly M Simon
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - António M Baptista
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - Peter Zuber
- NSF Science & Technology Center for Coastal Margin Observation & Prediction (CMOP), Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
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Smith MW, Herfort L, Fortunato CS, Crump BC, Simon HM. Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary. Microbiologyopen 2017; 6. [PMID: 28318115 PMCID: PMC5552926 DOI: 10.1002/mbo3.467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/02/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022] Open
Abstract
Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3‐μm prefilter and 0.2‐μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES‐5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES‐5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free‐living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low‐salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical “hotspot,” which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater–brackish water interface in the fast‐flowing Columbia River estuary.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | | | - Byron C Crump
- Oregon State University, College of Earth, Ocean and Atmospheric Sciences, Corvallis, OR, USA
| | - Holly M Simon
- Center for Coastal Margin Observation & Prediction, Oregon Health & Science University, Portland, OR, USA.,Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
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Jeffries TC, Schmitz Fontes ML, Harrison DP, Van-Dongen-Vogels V, Eyre BD, Ralph PJ, Seymour JR. Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary. Front Microbiol 2016; 6:1438. [PMID: 26858690 PMCID: PMC4726783 DOI: 10.3389/fmicb.2015.01438] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/02/2015] [Indexed: 02/01/2023] Open
Abstract
The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem.
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Affiliation(s)
- Thomas C. Jeffries
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney UniversityPenrith, NSW, Australia
| | - Maria L. Schmitz Fontes
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Daniel P. Harrison
- School of Geosciences, University of Sydney Institute of Marine Science, The University of SydneySydney, NSW, Australia
- Sydney Institute of Marine ScienceMosman, NSW, Australia
| | - Virginie Van-Dongen-Vogels
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Bradley D. Eyre
- Centre for Coastal Management, Southern Cross UniversityLismore, NSW, Australia
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
| | - Justin R. Seymour
- Plant Functional Biology and Climate Change Cluster, University of Technology SydneySydney, NSW, Australia
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Fortunato CS, Crump BC. Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient. PLoS One 2015; 10:e0140578. [PMID: 26536246 PMCID: PMC4633275 DOI: 10.1371/journal.pone.0140578] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/26/2015] [Indexed: 11/17/2022] Open
Abstract
Microbial communities mediate the biogeochemical cycles that drive ecosystems, and it is important to understand how these communities are affected by changing environmental conditions, especially in complex coastal zones. As fresh and marine waters mix in estuaries and river plumes, the salinity, temperature, and nutrient gradients that are generated strongly influence bacterioplankton community structure, yet, a parallel change in functional diversity has not been described. Metagenomic and metatranscriptomic analyses were conducted on five water samples spanning the salinity gradient of the Columbia River coastal margin, including river, estuary, plume, and ocean, in August 2010. Samples were pre-filtered through 3 μm filters and collected on 0.2 μm filters, thus results were focused on changes among free-living microbial communities. Results from metagenomic 16S rRNA sequences showed taxonomically distinct bacterial communities in river, estuary, and coastal ocean. Despite the strong salinity gradient observed over sampling locations (0 to 33), the functional gene profiles in the metagenomes were very similar from river to ocean with an average similarity of 82%. The metatranscriptomes, however, had an average similarity of 31%. Although differences were few among the metagenomes, we observed a change from river to ocean in the abundance of genes encoding for catabolic pathways, osmoregulators, and metal transporters. Additionally, genes specifying both bacterial oxygenic and anoxygenic photosynthesis were abundant and expressed in the estuary and plume. Denitrification genes were found throughout the Columbia River coastal margin, and most highly expressed in the estuary. Across a river to ocean gradient, the free-living microbial community followed three different patterns of diversity: 1) the taxonomy of the community changed strongly with salinity, 2) metabolic potential was highly similar across samples, with few differences in functional gene abundance from river to ocean, and 3) gene expression was highly variable and generally was independent of changes in salinity.
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Affiliation(s)
- Caroline S Fortunato
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Byron C Crump
- College of Earth, Oceans, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, United States of America
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Smith MW, Davis RE, Youngblut ND, Kärnä T, Herfort L, Whitaker RJ, Metcalf WW, Tebo BM, Baptista AM, Simon HM. Metagenomic evidence for reciprocal particle exchange between the mainstem estuary and lateral bay sediments of the lower Columbia River. Front Microbiol 2015; 6:1074. [PMID: 26483785 PMCID: PMC4589670 DOI: 10.3389/fmicb.2015.01074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/18/2015] [Indexed: 11/27/2022] Open
Abstract
Lateral bays of the lower Columbia River estuary are areas of enhanced water retention that influence net ecosystem metabolism through activities of their diverse microbial communities. Metagenomic characterization of sediment microbiota from three disparate sites in two brackish lateral bays (Baker and Youngs) produced ∼100 Gbp of DNA sequence data analyzed subsequently for predicted SSU rRNA and peptide-coding genes. The metagenomes were dominated by Bacteria. A large component of Eukaryota was present in Youngs Bay samples, i.e., the inner bay sediment was enriched with the invasive New Zealand mudsnail, Potamopyrgus antipodarum, known for high ammonia production. The metagenome was also highly enriched with an archaeal ammonia oxidizer closely related to Nitrosoarchaeum limnia. Combined analysis of sequences and continuous, high-resolution time series of biogeochemical data from fixed and mobile platforms revealed the importance of large-scale reciprocal particle exchanges between the mainstem estuarine water column and lateral bay sediments. Deposition of marine diatom particles in sediments near Youngs Bay mouth was associated with a dramatic enrichment of Bacteroidetes (58% of total Bacteria) and corresponding genes involved in phytoplankton polysaccharide degradation. The Baker Bay sediment metagenome contained abundant Archaea, including diverse methanogens, as well as functional genes for methylotrophy and taxonomic markers for syntrophic bacteria, suggesting that active methane cycling occurs at this location. Our previous work showed enrichments of similar anaerobic taxa in particulate matter of the mainstem estuarine water column. In total, our results identify the lateral bays as both sources and sinks of biogenic particles significantly impacting microbial community composition and biogeochemical activities in the estuary.
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Affiliation(s)
- Maria W Smith
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Richard E Davis
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | | | - Tuomas Kärnä
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - William W Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana IL, USA
| | - Bradley M Tebo
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - António M Baptista
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
| | - Holly M Simon
- Center for Coastal Margin Observation and Prediction and Institute of Environmental Health, Oregon Health & Science University, Portland OR, USA
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Simon HM, Smith MW, Herfort L. Metagenomic insights into particles and their associated microbiota in a coastal margin ecosystem. Front Microbiol 2014; 5:466. [PMID: 25250019 PMCID: PMC4155809 DOI: 10.3389/fmicb.2014.00466] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/17/2014] [Indexed: 11/17/2022] Open
Abstract
Our previously published research was one of the pioneering studies on the use of metagenomics to directly compare taxonomic and metabolic properties of aquatic microorganisms from different filter size-fractions. We compared size-fractionated water samples representing free-living and particle-attached communities from four diverse habitats in the Columbia River coastal margin, analyzing 12 metagenomes consisting of >5 million sequence reads (>1.6 Gbp). With predicted peptide and rRNA data we evaluated eukaryotic, bacterial and archaeal populations across size fractions and related their properties to attached and free-living lifestyles, and their potential roles in carbon and nutrient cycling. In this focused review, we expand our discussion on the use of high-throughput sequence data to relate microbial community structure and function to the origin, fate and transport of particulate organic matter (POM) in coastal margins. We additionally discuss the potential impact of the priming effect on organic matter cycling at the land-ocean interface, and build a case for the importance, in particle-rich estuaries and coastal margin waters, of microbial activities in low-oxygen microzones within particle interiors.
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Affiliation(s)
- Holly M Simon
- Center for Coastal Margin Observation and Prediction, Institute of Environmental Health, Oregon Health and Science University Portland, OR, USA
| | - Maria W Smith
- Center for Coastal Margin Observation and Prediction, Institute of Environmental Health, Oregon Health and Science University Portland, OR, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction, Institute of Environmental Health, Oregon Health and Science University Portland, OR, USA
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7
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A microarray for assessing transcription from pelagic marine microbial taxa. ISME JOURNAL 2014; 8:1476-91. [PMID: 24477198 DOI: 10.1038/ismej.2014.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 12/16/2013] [Accepted: 12/31/2013] [Indexed: 02/08/2023]
Abstract
Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.
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Skorupa DJ, Castenholz RW, Mazurie A, Carey C, Rosenzweig F, McDermott TR. In situ gene expression profiling of the thermoacidophilic alga Cyanidioschyzon in relation to visible and ultraviolet irradiance. Environ Microbiol 2013; 16:1627-41. [PMID: 24274381 DOI: 10.1111/1462-2920.12317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 10/20/2013] [Indexed: 02/04/2023]
Abstract
Ultraviolet and high-intensity visible radiation generate reactive intermediates that damage phototrophic microorganisms. In Yellowstone National Park, the thermoacidophilic alga Cyanidioschyzon exhibits an annual seasonal biomass fluctuation referred to as 'mat decline', where algal viability decreases as ultraviolet and visible irradiances increase during summer. We examined the role irradiance might play in mat decline using irradiance filters that uncouple ultraviolet and visible effects along with custom microarrays to study gene expression in situ. Of the 6507 genes, 88% showed no response to ultraviolet or visible, implying that at the biomolecular level, these algae inhabit a chemostat-like environment and is consistent with the near constant aqueous chemistry measured. The remaining genes exhibited expression changes linked to ultraviolet exposure, to increased visible radiation, or to the apparent combined effects of ultraviolet and visible. Expression of DNA repetitive elements was synchronized, being repressed by visible but also influenced by ultraviolet. At highest irradiance levels, these algae reduced transcription of genes encoding functions involved with DNA replication, photosynthesis and cell cycle progression but exhibited an uptick in activities related to repairing DNA damage. This corroborates known physiological responses to ultraviolet and visible radiation, and leads us to provisionally conclude that mat decline is linked to photoinhibition.
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Affiliation(s)
- Dana J Skorupa
- Department of Microbiology, Montana State University, Bozeman, MT, 59717, USA
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Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios. Appl Environ Microbiol 2013; 79:5338-44. [PMID: 23811506 DOI: 10.1128/aem.01031-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples.
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Smith MW, Zeigler Allen L, Allen AE, Herfort L, Simon HM. Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem. Front Microbiol 2013; 4:120. [PMID: 23750156 PMCID: PMC3668451 DOI: 10.3389/fmicb.2013.00120] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 04/29/2013] [Indexed: 11/22/2022] Open
Abstract
The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1-0.8, 0.8-3, and 3-200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2-10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.
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Affiliation(s)
- Maria W. Smith
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
| | - Lisa Zeigler Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Lydie Herfort
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
| | - Holly M. Simon
- Center for Coastal Margin Observation and Prediction, Oregon Health and Science UniversityBeaverton, OR, USA
- Division of Environmental and Biomolecular Systems, Department of Science and Engineering, Oregon Health and Science UniversityBeaverton, OR, USA
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Turk-Kubo KA, Achilles KM, Serros TRC, Ochiai M, Montoya JP, Zehr JP. Nitrogenase (nifH) gene expression in diazotrophic cyanobacteria in the Tropical North Atlantic in response to nutrient amendments. Front Microbiol 2012; 3:386. [PMID: 23130017 PMCID: PMC3487379 DOI: 10.3389/fmicb.2012.00386] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/17/2012] [Indexed: 11/30/2022] Open
Abstract
The Tropical North Atlantic (TNAtl) plays a critical role in the marine nitrogen cycle, as it supports high rates of biological nitrogen (N2) fixation, yet it is unclear whether this process is limited by the availability of iron (Fe), phosphate (P) or is co-limited by both. In order to investigate the impact of nutrient limitation on the N2-fixing microorganisms (diazotrophs) in the TNAtl, trace metal clean nutrient amendment experiments were conducted, and the expression of nitrogenase (nifH) in cyanobacterial diazotrophs in response to the addition of Fe, P, or Fe+P was measured using quantitative PCR. To provide context, N2 fixation rates associated with the <10 μm community and diel nifH expression in natural cyanobacterial populations were measured. In the western TNAtl, nifH expression in Crocosphaera, Trichodesmium, and Richelia was stimulated by Fe and Fe+P additions, but not by P, implying that diazotrophs may be Fe-limited in this region. In the eastern TNAtl, nifH expression in unicellular cyanobacteria UCYN-A and Crocosphaera was stimulated by P, implying P-limitation. In equatorial waters, nifH expression in Trichodesmium was highest in Fe+P treatments, implying co-limitation in this region. Nutrient additions did not measurably stimulate N2 fixation rates in the <10 μm fraction in most of the experiments, even when upregulation of nifH expression was evident. These results demonstrate the utility of using gene expression to investigate the physiological state of natural populations of microorganisms, while underscoring the complexity of nutrient limitation on diazotrophy, and providing evidence that diazotroph populations are slow to respond to the addition of limiting nutrients and may be limited by different nutrients on basin-wide spatial scales. This has important implications for our current understanding of controls on N2 fixation in the TNAtl and may partially explain why it appears to be intermittently limited by Fe, P, or both.
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Affiliation(s)
- Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California at Santa Cruz Santa Cruz, CA, USA
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Comparative analysis of 16S rRNA and amoA genes from archaea selected with organic and inorganic amendments in enrichment culture. Appl Environ Microbiol 2012; 78:2137-46. [PMID: 22267662 DOI: 10.1128/aem.06845-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We took advantage of a plant-root enrichment culture system to characterize mesophilic soil archaea selected through the use of organic and inorganic amendments. Comparative analysis of 16S rRNA and amoA genes indicated that specific archaeal clades were selected under different conditions. Three amoA sequence clades were identified, while for a fourth group, identified by 16S rRNA gene analysis alone and referred to as the "root" clade, we detected no corresponding amoA gene. The amoA-containing archaea were present in media with either organic or inorganic amendments, whereas archaea representing the root clade were present only when organic amendment was used. Analysis of amoA gene abundance and expression, together with nitrification-coupled growth assays, indicated potential growth by autotrophic ammonia oxidation for members of two group 1.1b clades. Increased abundance of one of these clades, however, also occurred upon the addition of organic amendment. Finally, although amoA-containing group 1.1a archaea were present in enrichments, we detected neither expression of amoA genes nor evidence for nitrification-coupled growth of these organisms. These data support a model of a diverse metabolic community in mesophilic soil archaea that is just beginning to be characterized.
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Silveira CB, Vieira RP, Cardoso AM, Paranhos R, Albano RM, Martins OB. Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean. PLoS One 2011; 6:e17789. [PMID: 21408023 PMCID: PMC3052384 DOI: 10.1371/journal.pone.0017789] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Accepted: 02/09/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. CONCLUSIONS/SIGNIFICANCE Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.
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Affiliation(s)
- Cynthia B. Silveira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ricardo P. Vieira
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexander M. Cardoso
- Instituto Nacional de Metrologia
Normalização e Qualidade Industrial, Rio de Janeiro,
Brazil
- * E-mail:
| | - Rodolfo Paranhos
- Instituto de Biologia, Universidade Federal do
Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodolpho M. Albano
- Departamento de Bioquímica,
Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando B. Martins
- Instituto de Bioquímica Médica,
Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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