Environmental Microbiology

Heath, Katy D.; Grillo, Michael A.

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13492pmid: 27507122

Chen, Tzong‐Yueh; Tai, Jen‐Hua; Ko, Chia‐Ying; Hsieh, Chih‐hao; Chen, Chung‐Chi; Jiao, Nianzhi; Liu, Hong‐Bin; Shiah, Fuh‐Kwo

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13273pmid: 26940842

This study demonstrated the potential effects of internal waves (IWs) on heterotrophic bacterial activities for the first time. Nine anchored studies were conducted from 2009–2012 in the South China Sea areas with different physical conditions, i.e. areas subjected to elevation IWs, to depression IWs, and to weak/no IWs. The latter two areas were treated as the Control sites. Field survey results indicated that within the euphotic zone, the minima of the depth‐averaged bacterial production (IBP; ∼1.0 mgC m−3 d−1) and growth rate (IBμ; ∼0.1 d−1) at all sites were similar. Except for one case, the maxima of IBP (6–12 mgC m−3 d−1) and IBμ (0.55–1.13 d−1) of the elevation IWs areas were ∼fivefolds higher than those of the Control sites (IBP 1.7–2.1 mgC m−3 d−1; IBμ 0.13–0.24 d−1). Replicate surveys conducted at the north‐western area of the Dongsha atoll during spring‐to‐neap (NW1 survey) and neap‐to‐spring (NW2 survey) tide periods showed a great contrast to each other. Low variation and averages of IBμ in NW1 survey were similar to those of the Control sites, while those in NW2 were similar to the other elevation IWs sites with larger variation and higher averages of IBμ. This finding suggests that bacterial activities may be a function of the lunar fortnightly (14‐day) cycle. Enrichment experiments suggested more directly that the limiting inorganic nutrients introduced by the elevation waves (EIWs) may contribute a higher IBμ within the euphotic zone.

Zhu, Chun; Wakeham, Stuart G.; Elling, Felix J.; Basse, Andreas; Mollenhauer, Gesine; Versteegh, Gerard J. M.; Könneke, Martin; Hinrichs, Kai‐Uwe

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13289pmid: 26950522

Membrane lipids of marine planktonic archaea have provided unique insights into archaeal ecology and paleoceanography. However, past studies of archaeal lipids in suspended particulate matter (SPM) and sediments mainly focused on a small class of fully saturated glycerol dibiphytanyl glycerol tetraether (GDGT) homologues identified decades ago. The apparent low structural diversity of GDGTs is in strong contrast to the high diversity of metabolism and taxonomy among planktonic archaea. Furthermore, adaptation of archaeal lipids in the deep ocean remains poorly constrained. We report the archaeal lipidome in SPM from diverse oceanic regimes. We extend the known inventory of planktonic archaeal lipids to include numerous unsaturated archaeal ether lipids (uns‐AELs). We further reveal (i) different thermal regulations and polar headgroup compositions of membrane lipids between the epipelagic (≤ 100 m) and deep (>100 m) populations of archaea, (ii) stratification of unsaturated GDGTs with varying redox conditions, and (iii) enrichment of tetra‐unsaturated archaeol and fully saturated GDGTs in epipelagic and deep oxygenated waters, respectively. Such stratified lipid patterns are consistent with the typical distribution of archaeal phylotypes in marine environments. We, thus, provide an ecological context for GDGT‐based paleoclimatology and bring about the potential use of uns‐AELs as biomarkers for planktonic Euryarchaeota.

Ledermann, Benjamin; Béjà, Oded; Frankenberg‐Dinkel, Nicole

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13290pmid: 26950653

The pink open‐chain tetrapyrrole pigment phycoerythrobilin (PEB) is employed by marine cyanobacteria, red algae and cryptophytes as a light‐harvesting chromophore in phycobiliproteins. Genes encoding biosynthesis proteins for PEB have also been discovered in cyanophages, viruses that infect cyanobacteria, and mimic host pigment biosynthesis with the exception of PebS which combines the enzymatic activities of two host enzymes. In this study, we have identified novel members of the PEB biosynthetic enzyme families, heme oxygenases and ferredoxin‐dependent bilin reductases. Encoding genes were found in metagenomic datasets and could be traced back to bacteriophage but not cyanophage origin. While the heme oxygenase exhibited standard activity, a new bilin reductase with highest homology to the teal pigment producing enzyme PcyA revealed PEB biosynthetic activity. Although PcyX possesses PebS‐like activity both enzymes share only 9% sequence identity and likely catalyze the reaction via two independent mechanisms. Our data point towards the presence of phycobilin biosynthetic genes in phages that probably infect alphaproteobacteria and, therefore, further support a role of phycobilins outside oxygenic phototrophs.

Meier, Dimitri V.; Bach, Wolfgang; Girguis, Peter R.; Gruber‐Vodicka, Harald R.; Reeves, Eoghan P.; Richter, Michael; Vidoudez, Charles; Amann, Rudolf; Meyerdierks, Anke

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13304pmid: 27001712

Deep‐sea hydrothermal vents are highly dynamic habitats characterized by steep temperature and chemical gradients. The oxidation of reduced compounds dissolved in the venting fluids fuels primary production providing the basis for extensive life. Until recently studies of microbial vent communities have focused primarily on chemolithoautotrophic organisms. In our study, we targeted the change of microbial community compositions along mixing gradients, focusing on distribution and capabilities of heterotrophic microorganisms. Samples were retrieved from different venting areas within the Menez Gwen hydrothermal field, taken along mixing gradients, including diffuse fluid discharge points, their immediate surroundings and the buoyant parts of hydrothermal plumes. High throughput 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization, and targeted metagenome analysis were combined with geochemical analyses. Close to diffuse venting orifices dominated by chemolithoautotrophic Epsilonproteobacteria, in areas where environmental conditions still supported chemolithoautotrophic processes, we detected microbial communities enriched for versatile heterotrophic Alpha‐ and Gammaproteobacteria. The potential for alkane degradation could be shown for several genera and yet uncultured clades. We propose that hotspots of chemolithoautotrophic life support a ‘belt’ of heterotrophic bacteria significantly different from the dominating oligotrophic microbiota of the deep sea.

Mitulla, Maximilian; Dinasquet, Julie; Guillemette, Ryan; Simon, Meinhard; Azam, Farooq; Wietz, Matthias

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13314pmid: 27059936

Alginate is a major cell wall polysaccharide from marine macroalgae and nutrient source for heterotrophic bacteria. Alginate can form gel particles in contact with divalent cations as found in seawater. Here, we tested the hypothesis that alginate gel particles serve as carbon source and microhabitat for marine bacteria by adding sterile alginate particles to microcosms with seawater from coastal California, a habitat rich in alginate‐containing macroalgae. Alginate particles were rapidly colonized and degraded, with three‐ to eightfold higher bacterial abundances and production among alginate particle‐associated (PA) bacteria. 16S rRNA gene amplicon sequencing showed that alginate PA bacteria were enriched in OTUs related to Cryomorphaceae, Saprospiraceae (Bacteroidetes) and Phaeobacter (Alphaproteobacteria) towards the end of the experiment. In microcosms amended with alginate particles and the proficient alginolytic bacterium Alteromonas macleodii strain 83‐1, this strain dominated the community and outcompeted Cryomorphaceae, Saprospiraceae and Phaeobacter, and PA hydrolytic activities were over 50% higher. Thus, alginolytic activity by strain 83‐1 did not benefit non‐alginolytic strains by cross‐feeding on alginate hydrolysis or other metabolic products. Considering the global distribution and extensive biomass of alginate‐containing macroalgae, the observed bacterial dynamics associated with the utilization and remineralization of alginate microhabitats promote the understanding of carbon cycling in macroalgae‐rich waters worldwide.

Severin, Tatiana; Sauret, Caroline; Boutrif, Mehdi; Duhaut, Thomas; Kessouri, Fayçal; Oriol, Louise; Caparros, Jocelyne; Pujo‐Pay, Mireille; Durrieu de Madron, Xavier; Garel, Marc; Tamburini, Christian; Conan, Pascal; Ghiglione, Jean‐François

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13324pmid: 27059603

Open‐ocean convection is a fundamental process for thermohaline circulation and biogeochemical cycles that causes spectacular mixing of the water column. Here, we tested how much the depth‐stratified prokaryotic communities were influenced by such an event, and also by the following re‐stratification. The deep convection event (0–1500 m) that occurred in winter 2010–2011 in the NW Mediterranean Sea resulted in a homogenization of the prokaryotic communities over the entire convective cell, resulting in the predominance of typical surface Bacteria, such as Oceanospirillale and Flavobacteriales. Statistical analysis together with numerical simulation of vertical homogenization evidenced that physical turbulence only was not enough to explain the new distribution of the communities, but acted in synergy with other parameters such as exported particulate and dissolved organic matters. The convection also stimulated prokaryotic abundance (+21%) and heterotrophic production (+43%) over the 0–1500 m convective cell, and resulted in a decline of cell‐specific extracellular enzymatic activities (−67%), thus suggesting an intensification of the labile organic matter turnover during the event. The rapid re‐stratification of the prokaryotic diversity and activities in the intermediate layer 5 days after the intense mixing indicated a marked resilience of the communities, apart from the residual deep mixed water patch.

Roth‐Schulze, Alexandra J.; Zozaya‐Valdés, Enrique; Steinberg, Peter D.; Thomas, Torsten

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13325pmid: 27062175

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host‐specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface‐associated life‐style, but also specific features that mediate host‐specificity.

Sildever, Sirje; Sefbom, Josefin; Lips, Inga; Godhe, Anna

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13372pmid: 27207672

It has been shown that the planktonic diatom Skeletonema from neighbouring areas are genetically differentiated despite absence of physical dispersal barriers. We revisited two sites, Mariager Fjord and Kattegat, NE Atlantic, and isolated new strains. Microsatellite genotyping and F‐statistics revealed that the populations were genetically differentiated. An experiment was designed to investigate if populations are locally adapted and have a native competitive advantage. Ten strains from each location were grown individually in native and foreign water to investigate differences in produced biomass. Additionally, we mixed six pairs, one strain from each site, and let them grow together in native and foreign water. Strains from Mariager Fjord and Kattegat produced higher biomass in native water. In the competition experiment, strains from both sites displayed higher relative abundance and demonstrated competitive advantage in their native water. The cause of the differentiated growth is unknown, but could possibly be attributed to differences in silica concentration or viruses in the two water types. Our data show that dispersal potential does not influence the genetic structure of the populations. We conclude that genetic adaptation has not been overruled by gene flow, but instead the responses to different selection conditions are enforcing the observed genetic structure.

Garrido, José L.; Brunet, Christophe; Rodríguez, Francisco

2016 Environmental Microbiology

doi: 10.1111/1462-2920.13373pmid: 27198623

Many studies on photoacclimation examine the pigment responses to changes in light intensity, but variations in light climate in the aquatic environment are also related to changes in spectral composition. We have employed a high‐performance liquid chromatography method with improved resolution towards chlorophyll c and fucoxanthin‐related xanthophylls to examine the pigment composition of Emiliania huxleyi CCMP 370 under different light intensities and spectral qualities.