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Muthusamy, S. D., Lundin, D., Branca, R. M., Baltar, F., Gonzalez, J. M., Lehtio, J. & Pinhassi, J. (2017). Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria. Environmental Microbiology, 19(6), 2301-2319
Open this publication in new window or tab >>Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria
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2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2301-2319Article, review/survey (Refereed) Published
Abstract [en]

Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2017
National Category
Microbiology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-66909 (URN)10.1111/1462-2920.13725 (DOI)000404007700018 ()
Available from: 2017-07-13 Created: 2017-07-13 Last updated: 2018-02-06Bibliographically approved
Bunse, C. & Pinhassi, J. (2017). Marine bacterioplankton seasonal succession dynamics. Trends in Microbiology, 25(6), 495-505
Open this publication in new window or tab >>Marine bacterioplankton seasonal succession dynamics
2017 (English)In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 25, no 6, p. 495-505Article in journal (Refereed) Published
Abstract [en]

Bacterioplankton (bacteria and archaea) are indispensable regulators of global element cycles owing to their unique ability to decompose and remineralize dissolved organic matter. These microorganisms in surface waters worldwide exhibit pronounced seasonal succession patterns, governed by physicochemical factors (e.g., light, climate, and nutrient loading) that are determined by latitude and distance to shore. Moreover, we emphasize that the effects of large-scale factors are modulated regionally, and over shorter timespans (days to weeks), by biological interactions including molecule exchanges, viral lysis, and grazing. Thus the interplay and scaling between factors ultimately determine the success of particular bacterial populations. Spatiotemporal surveys of bacterioplankton community composition provide the necessary frame for interpreting how the distinct metabolisms encoded in the genomes of different bacteria regulate biogeochemical cycles.

Place, publisher, year, edition, pages
Elsevier, 2017
National Category
Biological Sciences
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-60291 (URN)10.1016/j.tim.2016.12.013 (DOI)000401231800011 ()28108182 (PubMedID)
Projects
EcoChange
Available from: 2017-01-27 Created: 2017-01-27 Last updated: 2018-04-24Bibliographically approved
Lindh, M. V., Sjöstedt, J., Ekstam, B., Casini, M., Lundin, D., Hugerth, L., . . . Pinhassi, J. (2017). Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology, 19(3), 1222-1236
Open this publication in new window or tab >>Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
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2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 3, p. 1222-1236Article in journal (Refereed) Published
Abstract [en]

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2017
National Category
Ecology Microbiology
Research subject
Ecology, Microbiology; Natural Science, Ecology
Identifiers
urn:nbn:se:lnu:diva-61540 (URN)10.1111/1462-2920.13650 (DOI)000397525100031 ()28028880 (PubMedID)
Projects
EcoChange
Available from: 2017-03-21 Created: 2017-03-21 Last updated: 2018-04-24Bibliographically approved
Forss, J., Lindh, M. V., Pinhassi, J. & Welander, U. (2017). Microbial biotreatment of actual textile wastewater in a continuous sequential rice husk biofilter and the microbial community involved. PLoS ONE, 12(1), Article ID e0170562.
Open this publication in new window or tab >>Microbial biotreatment of actual textile wastewater in a continuous sequential rice husk biofilter and the microbial community involved
2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 1, article id e0170562Article in journal (Refereed) Published
Abstract [en]

Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments.

National Category
Water Treatment
Research subject
Technology (byts ev till Engineering), Environmental Biotechnology
Identifiers
urn:nbn:se:lnu:diva-61528 (URN)10.1371/journal.pone.0170562 (DOI)000396129000068 ()28114377 (PubMedID)
Available from: 2017-03-21 Created: 2017-03-21 Last updated: 2017-11-29Bibliographically approved
Broman, E., Sachpazidou, V., Pinhassi, J. & Dopson, M. (2017). Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism. Frontiers in Microbiology, 8, Article ID 2453.
Open this publication in new window or tab >>Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism
2017 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 2453Article in journal (Refereed) Published
Abstract [en]

The Baltic Sea has undergone severe eutrophication during the last century, resulting in increased algal blooms and the development of hypoxic bottom waters. In this study, we sampled oxygen deficient sediment cores from a Baltic Sea coastal bay and exposed the bottom water including the sediment surface to oxygen shifts via artificial addition of air during laboratory incubation. Surface sediment (top 1 cm) from the replicate cores were sliced in the field as well as throughout the laboratory incubations and chemical parameters were analyzed along with high throughput sequencing of community DNA and RNA. After oxygenation, dissolved iron decreased in the water overlying the sediment while inorganic sulfur compounds (thiosulfate and tetrathionate) increased when the water was kept anoxic. Oxygenation of the sediment also maintained RNA transcripts attributed to sulfide and sulfur oxidation as well as nitrogen fixation in the sediment surface. Based on 16S rRNA gene and metatranscriptomic analyses it was found that oxygenation of the sediment surface caused a bloom of the Epsilonproteobacteria genus Arcobacter. In addition, the formation of a thick white film was observed that was likely filamentous zero-valent sulfur produced by the Arcobacter spp. Based on these results, sulfur cycling and nitrogen fixation that were evident in the field samples were ongoing during re-oxygenation of the sediment. These processes potentially added organic nitrogen to the system and facilitated the re-establishment of micro- and macroorganism communities in the benthic zone.

National Category
Ecology
Research subject
Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-69514 (URN)10.3389/fmicb.2017.02453 (DOI)000417698300001 ()
Available from: 2017-12-30 Created: 2017-12-30 Last updated: 2018-01-31Bibliographically approved
Broman, E., Sjöstedt, J., Pinhassi, J. & Dopson, M. (2017). Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. Microbiome, 5, Article ID 96.
Open this publication in new window or tab >>Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism
2017 (English)In: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, article id 96Article in journal (Refereed) Published
Abstract [en]

Background

A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as ‘dead zones’. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface.

Results

Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation.

Conclusions

These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.

Place, publisher, year, edition, pages
BioMed Central, 2017
National Category
Ecology
Research subject
Ecology, Aquatic Ecology; Ecology, Microbiology
Identifiers
urn:nbn:se:lnu:diva-67205 (URN)10.1186/s40168-017-0311-5 (DOI)000407724600002 ()28793929 (PubMedID)
Projects
EcoChange
Available from: 2017-08-09 Created: 2017-08-09 Last updated: 2018-04-24Bibliographically approved
Baltar, F., Legrand, C. & Pinhassi, J. (2016). Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea. Biogeosciences, 13(9), 2815-2821
Open this publication in new window or tab >>Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea
2016 (English)In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 13, no 9, p. 2815-2821Article in journal (Refereed) Published
Abstract [en]

Extracellular enzymatic activities (EEA) are a crucial step on the degradation of organic matter. Dissolved (cell-free) extracellular enzymes in seawater can make up a significant contribution of the bulk EEA. However, the factors controlling the proportion of dissolved EEA in the marine environment remain unknown. Here we studied the seasonal changes in the proportion of dissolved relative to total EEA (of alkaline phosphatase [APase], β-glucosidase, [BGase], and leucine aminopeptidase, [LAPase]), in the Baltic Sea for 18 months. The proportio n of dissolved EEA ranged between 37-100%, 0-100%, 34-100% for APase, BGase and LAPase, respectively. A consistent seasonal pattern in the proportion of dissolved EEA was found among all the studied enzymes, with values up to 100% during winter and <40% du ring summer. A significant negative relation was found between the 21proportion of dissolved EEA and temperature, indicating that temperature might be a critical factor controlling the proportion of dissolved relative to total EEA in marine environments. Our results suggest a strong decoupling of hydrolysis rates from mi crobial dynamics in cold waters. This implies that under cold conditions, cell-free enzymes can contribute to substrate availability at large distances from the producing cell, increasing the dissociation between the hydrolysis of organic compounds and the actual microbes producing the enzymes. This also indicates that global warming could come to affect the hydrolysis of organic matter by reducing the hydrolytic activity of cell-free enzymes.

Place, publisher, year, edition, pages
Copernicus Publications, 2016
National Category
Ecology
Research subject
Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-49774 (URN)10.5194/bg-13-2815-2016 (DOI)000377277300014 ()2-s2.0-84969760880 (Scopus ID)
Projects
EcoChange
Available from: 2016-02-15 Created: 2016-02-15 Last updated: 2018-06-08Bibliographically approved
Sala, M. M., Aparicio, F. L., Balague, V., Boras, J. A., Borrull, E., Cardelus, C., . . . Marrase, C. (2016). Contrasting effects of ocean acidification on the microbial food web under different trophic conditions. ICES Journal of Marine Science, 73(3), 670-679
Open this publication in new window or tab >>Contrasting effects of ocean acidification on the microbial food web under different trophic conditions
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2016 (English)In: ICES Journal of Marine Science, ISSN 1054-3139, E-ISSN 1095-9289, Vol. 73, no 3, p. 670-679Article in journal (Refereed) Published
Abstract [en]

We investigated the effects of an increase in dissolved CO2 on the microbial communities of the Mediterranean Sea during two mesocosm experiments in two contrasting seasons: winter, at the peak of the annual phytoplankton bloom, and summer, under low nutrient conditions. The experiments included treatments with acidification and nutrient addition, and combinations of the two. We followed the effects of ocean acidification (OA) on the abundance of the main groups of microorganisms (diatoms, dinoflagellates, nanoeukaryotes, picoeukaryotes, cyanobacteria, and heterotrophic bacteria) and on bacterial activity, leucine incorporation, and extracellular enzyme activity. Our results showed a clear stimulation effect of OA on the abundance of small phytoplankton (pico- and nanoeukaryotes), independently of the season and nutrient availability. A large number of the measured variables showed significant positive effects of acidification in summer compared with winter, when the effects were sometimes negative. Effects of OA were more conspicuous when nutrient concentrations were low. Our results therefore suggest that microbial communities in oligotrophic waters are considerably affected by OA, whereas microbes in more productive waters are less affected. The overall enhancing effect of acidification on eukaryotic pico- and nanophytoplankton, in comparison with the non-significant or even negative response to nutrient-rich conditions of larger groups and autotrophic prokaryotes, suggests a shift towards medium-sized producers in a future acidified ocean.

Keywords
acidification, eutrophication, Mediterranean sea, mesocosm, microorganisms
National Category
Ecology
Research subject
Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-51066 (URN)10.1093/icesjms/fsv130 (DOI)000371142000017 ()2-s2.0-85021971448 (Scopus ID)
Available from: 2016-03-18 Created: 2016-03-18 Last updated: 2017-11-30Bibliographically approved
Brindefalk, B., Ekman, M., Ininbergs, K., Dupont, C. L., Yooseph, S., Pinhassi, J. & Bergman, B. (2016). Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters. Environmental Microbiology, 18(12), 4442-4455
Open this publication in new window or tab >>Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters
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2016 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, no 12, p. 4442-4455Article in journal (Refereed) Published
Abstract [en]

Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from similar to 0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 mu m), relative to the medium (0.8-3.0 mu m) and large (> 3.0 mu m) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.

National Category
Microbiology Ecology
Research subject
Ecology, Microbiology; Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-61150 (URN)10.1111/1462-2920.13407 (DOI)000392946900012 ()27306515 (PubMedID)2-s2.0-84978516857 (Scopus ID)
Projects
EcoChange
Available from: 2017-03-08 Created: 2017-03-08 Last updated: 2018-04-24Bibliographically approved
Vaquer-Sunyer, R., Reader, H. E., Muthusamy, S. D., Lindh, M. V., Pinhassi, J., Conley, D. J. & Kritzberg, E. S. (2016). Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea. Biogeosciences, 13(16), 4751-4765
Open this publication in new window or tab >>Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea
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2016 (English)In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 13, no 16, p. 4751-4765Article in journal (Refereed) Published
Abstract [en]

The Baltic Sea is the world's largest area suffering from eutrophication-driven hypoxia. Low oxygen levels are threatening its biodiversity and ecosystem functioning. The main causes for eutrophication-driven hypoxia are high nutrient loadings and global warming. Wastewater treatment plants (WWTP) contribute to eutrophication as they are important sources of nitrogen to coastal areas. Here, we evaluated the effects of wastewater treatment plant effluent inputs on Baltic Sea planktonic communities in four experiments. We tested for effects of effluent inputs on chlorophyll a content, bacterial community composition, and metabolic rates: gross primary production (GPP), net community production (NCP), community respiration (CR) and bacterial production (BP). Nitrogen-rich dissolved organic matter (DOM) inputs from effluents increased bacterial production and decreased primary production and community respiration. Nutrient amendments and seasonally variable environmental conditions lead to lower alpha-diversity and shifts in bacterial community composition (e.g. increased abundance of a few cyanobacterial populations in the summer experiment), concomitant with changes in metabolic rates. An increase in BP and decrease in CR could be caused by high lability of the DOM that can support secondary bacterial production, without an increase in respiration. Increases in bacterial production and simultaneous decreases of primary production lead to more carbon being consumed in the microbial loop, and may shift the ecosystem towards heterotrophy.

National Category
Ecology
Research subject
Ecology, Aquatic Ecology
Identifiers
urn:nbn:se:lnu:diva-57461 (URN)10.5194/bg-13-4751-2016 (DOI)000383799000003 ()2-s2.0-84983801370 (Scopus ID)
Available from: 2016-10-25 Created: 2016-10-19 Last updated: 2017-11-29Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-6405-1347

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