@article{PieckHerlemannJuergensetal.2015, author = {Pieck, Angelika and Herlemann, Daniel P. P. and Juergens, Klaus and Grossart, Hans-Peter}, title = {Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea}, series = {Frontiers in microbiology}, volume = {6}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2015.01297}, pages = {13}, year = {2015}, abstract = {Many studies on bacterial community composition (BCC) do not distinguish between particle associated (PA) and free-living (FL) bacteria or neglect the PA fraction by pre-filtration removing most particles. Although temporal and spatial gradients in environmental variables are known to shape BCC, it remains unclear how and to what extent PA and FL bacterial diversity responds to such environmental changes. To elucidate the BCC of both bacterial fractions related to different environmental settings, we studied surface samples of three Baltic Sea stations (marine, mesohaline, and oligohaline) in two different seasons (summer and fall/winter). Amplicon sequencing of the 16S rRNA gene revealed significant differences in BCC of both bacterial fractions among stations and seasons, with a particularly high number of PA operational taxonomic units (OTUs at genus-level) at the marine station in both seasons. "Shannon and Simpson indices" showed a higher diversity of PA than FL bacteria at the marine station in both seasons and at the oligohaline station in fall/winter. In general, a high fraction of bacterial OTUs was found exclusively in the PA fraction (52\% of total OTUs). These findings indicate that PA bacteria significantly contribute to overall bacterial richness and that they differ from FL bacteria. Therefore, to gain a deeper understanding on diversity and dynamics of aquatic bacteria, PA and FL bacteria should be generally studied independently.}, language = {en} } @article{FrindteAllgaierGrossartetal.2015, author = {Frindte, Katharina and Allgaier, Martin and Grossart, Hans-Peter and Eckert, Werner}, title = {Microbial response to experimentally controlled redox transitions at the sediment water interface}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {11}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0143428}, pages = {17}, year = {2015}, abstract = {The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.}, language = {en} } @article{DubovskayaTangGladyshevetal.2015, author = {Dubovskaya, Olga P. and Tang, Kam W. and Gladyshev, Michail I. and Kirillin, Georgiy and Buseva, Zhanna and Kasprzak, Peter and Tolomeev, Aleksandr P. and Grossart, Hans-Peter}, title = {Estimating In Situ Zooplankton Non-Predation Mortality in an Oligo-Mesotrophic Lake from Sediment Trap Data: Caveats and Reality Check}, series = {PLoS one}, volume = {10}, journal = {PLoS one}, number = {7}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131431}, pages = {17}, year = {2015}, abstract = {Background Mortality is a main driver in zooplankton population biology but it is poorly constrained in models that describe zooplankton population dynamics, food web interactions and nutrient dynamics. Mortality due to non-predation factors is often ignored even though anecdotal evidence of non-predation mass mortality of zooplankton has been reported repeatedly. One way to estimate non-predation mortality rate is to measure the removal rate of carcasses, for which sinking is the primary removal mechanism especially in quiescent shallow water bodies. Objectives and Results We used sediment traps to quantify in situ carcass sinking velocity and non-predation mortality rate on eight consecutive days in 2013 for the cladoceran Bosmina longirostris in the oligo-mesotrophic Lake Stechlin; the outcomes were compared against estimates derived from in vitro carcass sinking velocity measurements and an empirical model correcting in vitro sinking velocity for turbulence resuspension and microbial decomposition of carcasses. Our results show that the latter two approaches produced unrealistically high mortality rates of 0.58-1.04 d(-1), whereas the sediment trap approach, when used properly, yielded a mortality rate estimate of 0.015 d(-1), which is more consistent with concurrent population abundance data and comparable to physiological death rate from the literature. Ecological implications Zooplankton carcasses may be exposed to water column microbes for days before entering the benthos; therefore, non-predation mortality affects not only zooplankton population dynamics but also microbial and benthic food webs. This would be particularly important for carbon and nitrogen cycles in systems where recurring mid-summer decline of zooplankton population due to non-predation mortality is observed.}, language = {en} } @article{GludGrossartLarsenetal.2015, author = {Glud, Ronnie N. and Grossart, Hans-Peter and Larsen, Morten and Tang, Kam W. and Arendt, Kristine E. and Rysgaard, Soren and Thamdrup, Bo and Gissel Nielsen, Torkel}, title = {Copepod carcasses as microbial hot spots for pelagic denitrification}, series = {Limnology and oceanography}, volume = {60}, journal = {Limnology and oceanography}, number = {6}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.10149}, pages = {2026 -- 2036}, year = {2015}, abstract = {Copepods are exposed to a high non-predatory mortality and their decomposing carcasses act as microniches with intensified microbial activity. Sinking carcasses could thereby represent anoxic microenvironment sustaining anaerobic microbial pathways in otherwise oxic water columns. Using non-invasive O-2 imaging, we document that carcasses of Calanus finmarchicus had an anoxic interior even at fully air-saturated ambient O-2 level. The extent of anoxia gradually expanded with decreasing ambient O-2 levels. Concurrent microbial sampling showed the expression of nitrite reductase genes (nirS) in all investigated carcass samples and thereby documented the potential for microbial denitrification in carcasses. The nirS gene was occasionally expressed in live copepods, but not as consistently as in carcasses. Incubations of sinking carcasses in (15)NO3-amended seawater demonstrated denitrification, of which on average 34\%+/- 17\% (n=28) was sustained by nitrification. However, the activity was highly variable and was strongly dependent on the ambient O-2 levels. While denitrification was present even at air-saturation (302 mol L-1), the average carcass specific activity increased several orders of magnitude to approximate to 1 nmol d(-1) at 20\% air-saturation (55 mol O-2 L-1) at an ambient temperature of 7 degrees C. Sinking carcasses of C. finmarchicus therefore represent hotspots of pelagic denitrification, but the quantitative importance as a sink for bioavailable nitrogen is strongly dependent on the ambient O-2 level. The importance of carcass associated denitrification could be highly significant in O-2 depleted environments such as Oxygen Minimum Zones (OMZ).}, language = {en} } @article{BizicIonescuZederIonescuetal.2015, author = {Bizic-Ionescu, Mina and Zeder, Michael and Ionescu, Danny and Orlic, Sandi and Fuchs, Bernhard M. and Grossart, Hans-Peter and Amann, Rudolf}, title = {Comparison of bacterial communities on limnic versus coastal marine particles reveals profound differences in colonization}, series = {Environmental microbiology}, volume = {17}, journal = {Environmental microbiology}, number = {10}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.12466}, pages = {3500 -- 3514}, year = {2015}, abstract = {Marine and limnic particles are hotspots of organic matter mineralization significantly affecting biogeochemical element cycling. Fluorescence in-situ hybridization and pyrosequencing of 16S rRNA genes were combined to investigate bacterial diversity and community composition on limnic and coastal marine particles >5 and >10m respectively. Limnic particles were more abundant (average: 1x10(7)l(-1)), smaller in size (average areas: 471 versus 2050m(2)) and more densely colonized (average densities: 7.3 versus 3.6 cells 100m(-2)) than marine ones. Limnic particle-associated (PA) bacteria harboured Alphaproteobacteria and Betaproteobacteria, and unlike previously suggested sizeable populations of Gammaproteobacteria, Actinobacteria and Bacteroidetes. Marine particles were colonized by Planctomycetes and Betaproteobacteria additionally to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. Large differences in individual particle colonization could be detected. High-throughput sequencing revealed a significant overlap of PA and free-living (FL) bacteria highlighting an underestimated connectivity between both fractions. PA bacteria were in 14/21 cases more diverse than FL bacteria, reflecting a high heterogeneity in the particle microenvironment. We propose that a ratio of Chao 1 indices of PA/FL<1 indicates the presence of rather homogeneously colonized particles. The identification of different bacterial families enriched on either limnic or marine particles demonstrates that, despite the seemingly similar ecological niches, PA communities of both environments differ substantially.}, language = {en} } @article{GarciaBuckMcMahonetal.2015, author = {Garcia, Sarahi L. and Buck, Moritz and McMahon, Katherine D. and Grossart, Hans-Peter and Eiler, Alexander and Warnecke, Falk}, title = {Auxotrophy and intrapopulation complementary in the "interactome' of a cultivated freshwater model community}, series = {Molecular ecology}, volume = {24}, journal = {Molecular ecology}, number = {17}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.13319}, pages = {4449 -- 4459}, year = {2015}, abstract = {Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.}, language = {en} } @article{IonescuBizicIonescuKhalilietal.2015, author = {Ionescu, Danny and Bizic-Ionescu, Mina and Khalili, Arzhang and Malekmohammadi, Reza and Morad, Reza Mohammad and de Beer, Dirk and Grossart, Hans-Peter}, title = {A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect}, series = {Scientific reports}, volume = {5}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep14706}, pages = {12}, year = {2015}, abstract = {Downward fluxes of particulate organic matter (POM) are the major process for sequestering atmospheric CO2 into aquatic sediments for thousands of years. Budget calculations of the biological carbon pump are heavily based on the ratio between carbon export (sedimentation) and remineralization (release to the atmosphere). Current methodologies determine microbial dynamics on POM using closed vessels, which are strongly biased towards heterotrophy due to rapidly changing water chemistry (Bottle Effect). We developed a flow-through rolling tank for long term studies that continuously maintains POM at near in-situ conditions. There, bacterial communities resembled in-situ communities and greatly differed from those in the closed systems. The active particle-associated community in the flow-through system was stable for days, contrary to hours previously reported for closed incubations. In contrast to enhanced respiration rates, the decrease in photosynthetic rates on particles throughout the incubation was much slower in our system than in traditional ones. These results call for reevaluating experimentally-derived carbon fluxes estimated using traditional methods.}, language = {en} } @article{WannickeFrindteGustetal.2015, author = {Wannicke, Nicola and Frindte, Katharina and Gust, Giselher and Liskow, Iris and Wacker, Alexander and Meyer, Andreas and Grossart, Hans-Peter}, title = {Measuring bacterial activity and community composition at high hydrostatic pressure using a novel experimental approach: a pilot study}, series = {FEMS microbiology ecology}, volume = {91}, journal = {FEMS microbiology ecology}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0168-6496}, doi = {10.1093/femsec/fiv036}, pages = {15}, year = {2015}, abstract = {In this pilot study, we describe a high-pressure incubation system allowing multiple subsampling of a pressurized culture without decompression. The system was tested using one piezophilic (Photobacterium profundum), one piezotolerant (Colwellia maris) bacterial strain and a decompressed sample from the Mediterranean deep sea (3044 m) determining bacterial community composition, protein production (BPP) and cell multiplication rates (BCM) up to 27 MPa. The results showed elevation of BPP at high pressure was by a factor of 1.5 +/- 1.4 and 3.9 +/- 2.3 for P. profundum and C. maris, respectively, compared to ambient-pressure treatments and by a factor of 6.9 +/- 3.8 fold in the field samples. In P. profundum and C. maris, BCM at high pressure was elevated (3.1 +/- 1.5 and 2.9 +/- 1.7 fold, respectively) compared to the ambient-pressure treatments. After 3 days of incubation at 27 MPa, the natural bacterial deep-sea community was dominated by one phylum of the genus Exiguobacterium, indicating the rapid selection of piezotolerant bacteria. In future studies, our novel incubation system could be part of an isopiestic pressure chain, allowing more accurate measurement of bacterial activity rates which is important both for modeling and for predicting the efficiency of the oceanic carbon pump.}, language = {en} } @article{IshidaNozakiGrossartetal.2015, author = {Ishida, Seiji and Nozaki, Daiki and Grossart, Hans-Peter and Kagami, Maiko}, title = {Novel basal, fungal lineages from freshwater phytoplankton and lake samples}, series = {Environmental microbiology reports}, volume = {7}, journal = {Environmental microbiology reports}, number = {3}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12268}, pages = {435 -- 441}, year = {2015}, abstract = {Zoosporic fungal parasites are known to control the extent and development of blooms of numerous phytoplankton species. Despite the obvious importance of ecological interactions between parasitic fungi and their phytoplanktonic hosts, their diversity remains largely unknown due to methodological limitations. Here, a method to genetically analyse fungi directly from single, infected colonies of the phytoplanktonic host was applied to field samples of large diatom species from mesotrophic Lake Biwa and eutrophic Lake Inba, Japan. Although previous research on interaction between lacustrine fungi and large phytoplankton has mainly focused on the role of parasitic Chytridiomycota, our results revealed that fungi attached to large diatoms included not only members of Chytridiomycota, but also members of Aphelida, Cryptomycota and yeast. The fungi belonging to Chytridiomycota and Aphelida form novel, basal lineages. Environmental clone libraries also support the occurrence of these lineages in Japanese lakes. The presented method enables us to better characterize individual fungal specimens on phytoplankton, and thus facilitate and improve the investigation of ecological relationships between fungi and phytoplankton in aquatic ecosystems.}, language = {en} } @article{AttermeyerTittelAllgaieretal.2015, author = {Attermeyer, Katrin and Tittel, Joerg and Allgaier, Martin and Frindte, Katharina and Wurzbacher, Christian and Hilt, Sabine and Kamjunke, Norbert and Grossart, Hans-Peter}, title = {Effects of Light and Autochthonous Carbon Additions on Microbial Turnover of Allochthonous Organic Carbon and Community Composition}, series = {Microbial ecology}, volume = {69}, journal = {Microbial ecology}, number = {2}, publisher = {Springer}, address = {New York}, issn = {0095-3628}, doi = {10.1007/s00248-014-0549-4}, pages = {361 -- 371}, year = {2015}, abstract = {The fate of allochthonous dissolved organic carbon (DOC) in aquatic systems is primarily controlled by the turnover of heterotrophic bacteria. However, the roles that abiotic and biotic factors such as light and DOC release by aquatic primary producers play in the microbial decomposition of allochthonous DOC is not well understood. We therefore tested if light and autochthonous DOC additions would increase allochthonous DOC decomposition rates and change bacterial growth efficiencies and community composition (BCC). We established continuous growth cultures with different inocula of natural bacterial communities and alder leaf leachates (DOCleaf) with and without light exposure before amendment. Furthermore, we incubated DOCleaf together with autochthonous DOC from lysed phytoplankton cultures (DOCphyto). Our results revealed that pretreatments of DOCleaf with light resulted in a doubling of bacterial growth efficiency (BGE), whereas additions of DOCphyto or combined additions of DOCphyto and light had no effect on BGE. The change in BGE was not accompanied by shifts in the phylogenetic structure of the BCC, but BCC was influenced by the DOC source. Our results highlight that a doubling of BGE is not necessarily accompanied by a shift in BCC and that BCC is more strongly affected by resource properties.}, language = {en} }