TY  - JOUR
A1  - Balint, Miklos
A1  - Marton, Orsolya
A1  - Schatz, Marlene
A1  - Düring, Rolf-Alexander
A1  - Grossart, Hans-Peter
T1  - Proper experimental design requires randomization/balancing of molecular ecology experiments
JF  - Ecology and evolution
N2  - Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.
KW  - batch effect
KW  - bias
KW  - DNA extraction
KW  - environmental DNA
KW  - laboratory practice
KW  - lake community
KW  - metabarcoding
KW  - nondemonic intrusions
KW  - PCR
KW  - sediment
Y1  - 2018
U6  - https://doi.org/10.1002/ece3.3687
SN  - 2045-7758
VL  - 8
IS  - 3
SP  - 1786
EP  - 1793
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Bizic-Ionescu, Mina
A1  - Ionescu, Danny
A1  - Grossart, Hans-Peter
T1  - Organic Particles: Heterogeneous Hubs for Microbial Interactions in Aquatic Ecosystems
JF  - Frontiers in microbiology
N2  - The dynamics and activities of microbes colonizing organic particles (hereafter particles) greatly determine the efficiency of the aquatic carbon pump. Current understanding is that particle composition, structure and surface properties, determined mostly by the forming organisms and organic matter, dictate initial microbial colonization and the subsequent rapid succession events taking place as organic matter lability and nutrient content change with microbial degradation. We applied a transcriptomic approach to assess the role of stochastic events on initial microbial colonization of particles. Furthermore, we asked whether gene expression corroborates rapid changes in carbon-quality. Commonly used size fractionated filtration averages thousands of particles of different sizes, sources, and ages. To overcome this drawback, we used replicate samples consisting each of 3–4 particles of identical source and age and further evaluated the consequences of averaging 10–1000s of particles. Using flow-through rolling tanks we conducted long-term experiments at near in situ conditions minimizing the biasing effects of closed incubation approaches often referred to as “the bottle-effect.” In our open flow-through rolling tank system, however, active microbial communities were highly heterogeneous despite an identical particle source, suggesting random initial colonization. Contrasting previous reports using closed incubation systems, expression of carbon utilization genes didn’t change after 1 week of incubation. Consequently, we suggest that in nature, changes in particle-associated community related to carbon availability are much slower (days to weeks) due to constant supply of labile, easily degradable organic matter. Initial, random particle colonization seems to be subsequently altered by multiple organismic interactions shaping microbial community interactions and functional dynamics. Comparative analysis of thousands particles pooled togethers as well as pooled samples suggests that mechanistic studies of microbial dynamics should be done on single particles. The observed microbial heterogeneity and inter-organismic interactions may have important implications for evolution and biogeochemistry in aquatic systems.
KW  - particle-associated bacteria
KW  - microbial communities
KW  - inter- and intra-species interactions
KW  - antagonism
KW  - phage
KW  - transcriptome
Y1  - 2018
U6  - https://doi.org/10.3389/fmicb.2018.02569
SN  - 1664-302X
VL  - 9
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Wurzbacher, Christian
A1  - Fuchs, Andrea
A1  - Attermeyer, Katrin
A1  - Frindte, Katharina
A1  - Grossart, Hans-Peter
A1  - Hupfer, Michael
A1  - Casper, Peter
A1  - Monaghan, Michael T.
T1  - Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment
JF  - Microbiome
N2  - Background: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to Cs-137 dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results: Community beta-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.
KW  - Archaea
KW  - Eukaryota
KW  - Bacteria
KW  - Community
KW  - Freshwater
KW  - Lake
KW  - DNA metabarcoding
KW  - Beta-diversity
KW  - Sediment
KW  - Turnover
Y1  - 2017
U6  - https://doi.org/10.1186/s40168-017-0255-9
SN  - 2049-2618
VL  - 5
PB  - BioMed Central
CY  - London
ER  - 
TY  - JOUR
A1  - Göritz, Anna
A1  - Berger, Stella A.
A1  - Gege, Peter
A1  - Grossart, Hans-Peter
A1  - Nejstgaard, Jens C.
A1  - Riedel, Sebastian
A1  - Röttgers, Rüdiger
A1  - Utschig, Christian
T1  - Retrieval of water constituents from hyperspectral in-situ measurements under variable cloud cover
BT  - a case study at Lake Stechlin (Germany)
JF  - Remote sensing / Molecular Diversity Preservation International (MDPI)
N2  - Remote sensing and field spectroscopy of natural waters is typically performed under clear skies, low wind speeds and low solar zenith angles. Such measurements can also be made, in principle, under clouds and mixed skies using airborne or in-situ measurements; however, variable illumination conditions pose a challenge to data analysis. In the present case study, we evaluated the inversion of hyperspectral in-situ measurements for water constituent retrieval acquired under variable cloud cover. First, we studied the retrieval of Chlorophyll-a (Chl-a) concentration and colored dissolved organic matter (CDOM) absorption from in-water irradiance measurements. Then, we evaluated the errors in the retrievals of the concentration of total suspended matter (TSM), Chl-a and the absorption coefficient of CDOM from above-water reflectance measurements due to highly variable reflections at the water surface. In order to approximate cloud reflections, we extended a recent three-component surface reflectance model for cloudless atmospheres by a constant offset and compared different surface reflectance correction procedures. Our findings suggest that in-water irradiance measurements may be used for the analysis of absorbing compounds even under highly variable weather conditions. The extended surface reflectance model proved to contribute to the analysis of above-water reflectance measurements with respect to Chl-a and TSM. Results indicate the potential of this approach for all-weather monitoring.
KW  - remote sensing
KW  - inland water
KW  - hyperspectral measurements
KW  - in-situ
KW  - cloud
KW  - surface reflection
KW  - inversion
KW  - bio-optical modeling
Y1  - 2018
U6  - https://doi.org/10.3390/rs10020181
SN  - 2072-4292
VL  - 10
IS  - 2
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Cuadrat, Rafael R. C.
A1  - Ionescu, Danny
A1  - Davila, Alberto M. R.
A1  - Grossart, Hans-Peter
T1  - Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics
JF  - Frontiers in microbiology
N2  - Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
KW  - metagenomics 2.0
KW  - PKS
KW  - NRPS
KW  - freshwater
KW  - environmental genomics
Y1  - 2018
U6  - https://doi.org/10.3389/fmicb.2018.00251
SN  - 1664-302X
VL  - 9
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Xiao, Shangbin
A1  - Liu, Liu
A1  - Wang, Wei
A1  - Lorke, Andreas
A1  - Woodhouse, Jason Nicholas
A1  - Grossart, Hans-Peter
T1  - A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water
JF  - Hydrology and earth system sciences : HESS
N2  - Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6% and a measurement accuracy of 0.5% for CH4. A similar performance was observed for dissolved CO2 (t(95%) = 10 s, equilibration ratio 67.1 %). An equilibration ratio as high as 91.8% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.
Y1  - 2020
U6  - https://doi.org/10.5194/hess-24-3871-2020
SN  - 1027-5606
SN  - 1607-7938
VL  - 24
IS  - 7
SP  - 3871
EP  - 3880
PB  - European Geosciences Union (EGU) ; Copernicus
CY  - Munich
ER  - 
TY  - JOUR
A1  - Hoke, Alexa
A1  - Woodhouse, Jason Nicholas
A1  - Zoccarato, Luca
A1  - McCarthy, Valerie
A1  - de Eyto, Elvira
A1  - Caldero-Pascual, Maria
A1  - Geffroy, Ewan
A1  - Dillane, Mary
A1  - Grossart, Hans-Peter
A1  - Jennings, Eleanor
T1  - Impacts of extreme weather events on bacterial community composition of a temperate humic lake
JF  - Water
N2  - Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.
KW  - extreme weather event
KW  - storm
KW  - drought
KW  - bacteria
KW  - free-living
KW  - particle-associated
KW  - humic lake
Y1  - 2020
U6  - https://doi.org/10.3390/w12102757
SN  - 2073-4441
VL  - 12
IS  - 10
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Schellenberg, Johannes
A1  - Reichert, Jessica
A1  - Hardt, Martin
A1  - Klingelhöfer, Ines
A1  - Morlock, Gertrud
A1  - Schubert, Patrick
A1  - Bižić, Mina
A1  - Grossart, Hans-Peter
A1  - Kämpfer, Peter
A1  - Wilke, Thomas
A1  - Glaeser, Stefanie P.
T1  - The bacterial microbiome of the long-term aquarium cultured high-microbial abundance sponge Haliclona cnidata
BT  - sustained bioactivity despite community shifts under detrimental conditions
JF  - Frontiers in Marine Science
N2  - Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.
KW  - HMA sponge
KW  - bacterial symbionts
KW  - holobiont
KW  - antimicrobial defense
KW  - quorum sensing
KW  - bacteriocytes
Y1  - 2020
U6  - https://doi.org/10.3389/fmars.2020.00266
SN  - 2296-7745
VL  - 7
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Huang, Lixing
A1  - Qiao, Ying
A1  - Xu, Wei
A1  - Gong, Linfeng
A1  - He, Rongchao
A1  - Qi, Weilu
A1  - Gao, Qiancheng
A1  - Cai, Hongyan
A1  - Grossart, Hans-Peter
A1  - Yan, Qingpi
T1  - Full-length transcriptome
BT  - a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome
JF  - Frontiers in immunology
N2  - Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.
KW  - scRNA-seq
KW  - full-length transcriptome
KW  - immune cell population
KW  - teleost
KW  - infection
Y1  - 2021
U6  - https://doi.org/10.3389/fimmu.2021.737332
SN  - 1664-3224
VL  - 12
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Aichner, Bernhard
A1  - Dubbert, David
A1  - Kiel, Christine
A1  - Kohnert, Katrin
A1  - Ogashawara, Igor
A1  - Jechow, Andreas
A1  - Harpenslager, Sarah-Faye
A1  - Hölker, Franz
A1  - Nejstgaard, Jens Christian
A1  - Grossart, Hans-Peter
A1  - Singer, Gabriel
A1  - Wollrab, Sabine
A1  - Berger, Stella Angela
T1  - Spatial and seasonal patterns of water isotopes in northeastern German lakes
JF  - Earth system science data : ESSD
N2  - Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Y1  - 2022
U6  - https://doi.org/10.5194/essd-14-1857-2022
SN  - 1866-3508
SN  - 1866-3516
VL  - 14
IS  - 4
SP  - 1857
EP  - 1867
PB  - Copernicus
CY  - Göttingen
ER  -