Biology subjects

Busch, K.

Publications and source records attributed to Busch, K..

11 recordsLinked to original sources

bioRxiv2024

Dissolved organic matter fluxes and fatty acid composition from shallow-water and deep-water demo- and hexactinellid sponges from New Zealand

Sponges are an important component of shallow- and deep-water ecosystems enhancing eukaryotic biodiversity via diverse endo- and epibiota and by providing three dimensional habitats for benthic invertebrates and fishes. Sponge biodiversity is particularly high in the waters around New Zealand (Southwest Pacific), where we collected two shallow- and two deep-water sponge species (Tedania sp., Suberea meandrina, Farrea raoulensis, Artemisina sp.) for ex-situ incubation experiments to detect whether these sponges may process dissolved organic matter. We assessed the biochemical and phospholipid-derived fatty acids (PLFAs) and measured dissolved organic carbon (DOC) and total dissolved nitrogen (TDN) fluxes. Changes in fluorescent dissolved organic matter (FDOM) over time were analyzed and the results were linked to the bacterial communities of the sponge holobiont. Dried sponge tissue consisted of 17.5 {+/-} 3.75% organic (org.) C and of 4.34 {+/-} 1.02% total nitrogen (TN) with a natural stable isotope composition of -19.0 {+/-}0.25{per thousand} for {delta}13org. C and of 10.2 {+/-}2.43{per thousand} for {delta}15TN. None of the DOC fluxes was significant and only the release of TDN by Tedania sp. was significantly different from 0 mol TDN g org. C-1 d-1. We detected the presence of four fluorophores in the FDOM pool: 2 tryptophan- and protein-like fluorophores (C1, C2), 1 humic-like fluorophore (C3), and 1 tyrosine-like fluorophore (C4). The maximum fluorescence intensity Fmax of C1 decreased significantly in S. meandrina incubations, whereas Fmax of C2 grew in the same incubations. Fmax of C3 increased in Tedania sp. incubations, in which Fmax of C4 decreased. In comparison, Fmax of C4 in S. meandrina rose. The PLFA composition of sponge tissue was dominated by long-chain fatty acids, saturated fatty acids, and monosaturated fatty acids and most PLFAs were sponge- and bacteria-specific. The bacterial community of the demosponges Artemisina sp., S. meandrina and Tedania sp. consisted mostly of Proteobacteria and Chloroflexota, whereas the dominating bacteria phylum of the hexactinellid F. raoulensis was Proteobacteria. We proposed that the holobionts of S. meandrina and Tedania sp. contain bacteria that are involved in the transformation and degradation of DOM. In S. meandrina, Chloroflexota and Poribacteria may degrade tryptophan-like fluorophores to a chemically modified tryptophan-like and protein-like fluorophore, while producing a tyrosine-like fluorophore. In Tedania sp., Chloroflexota may contribute to the release of significant amounts of TDN by producing humic-like fluorophores, while degrading tyrosine-like fluorophores. Farrea raoulensis may not take up DOM due to a lack of Poribacteria and Chloroflexota or may use colloidal instead of truly dissolved DOC.

ecology↗

bioRxiv2024

Nutrient fluxes, oxygen consumption and fatty acid composition from deep-water demo- and hexactinellid sponges from New Zealand

Sponges are an important component of deep-water ecosystems enhancing eukaryotic biodiversity by hosting diverse endo- and epibiota and providing three dimensional habitats for benthic invertebrates and fishes. As holobionts they are important hosts of microorganisms which are involved in carbon and nitrogen cycling. While increasing exploration of deep-water habitats results in new sponge species being discovered, little is known about their physiology and role in nutrient fluxes. Around New Zealand (Southwest Pacific), the sponge biodiversity is particularly high, and we selected six deep-sea sponge clusters (Saccocalyx, Suberites, Tedania, Halichondria/ Dendoricella, Sceptrulophora, Lissodendoryx) for in-situ and ex-situ experiments. We investigated the biochemical composition of the sponges, measured oxygen consumption and inorganic nutrient fluxes, as well as bacterial and phospholipid-derived fatty acid (PLFA) compositions. Our aim was to assess differences in fluxes and fatty acid composition among sponge clusters and linking their bacterial communities to nitrogen cycling processes. All sponges excreted nitrite and ammonia. Nitrate and phosphate excretion were independent of phylum affiliation (Demospongiae, Hexactinellida). Nitrate was excreted by the Halichondria/ Dendoricella and Lissodendoryx clusters, whereas the Suberites, Tedania, and Sceptrulophora clusters consumed it. Phosphate was excreted by Sceptrulophora and Halichondria/ Dendoricella clusters and consumed by all other clusters. Silicon was consumed by all sponge clusters, except for Saccocalyx and Halichondria/ Dendoricella clusters. Oxygen consumption rates ranged from 0.17 to 3.56{+/-}0.60 mmol O2 g C d-1. The PLFA composition was very sponge-cluster dependent and consisted mostly of long-chain fatty acids. Most PLFAs were sponge-specific, followed by bacteria-specific PLFAs, and others. All sponge clusters, except for Suberites, were low-microbial abundance (LMA) sponges whose bacterial community composition was dominated by Proteobacteria, Bacteroidota, Planctomycetota, and Nitrospinota. The Suberites cluster consisted of high-microbial abundance (HMA) sponges with Proteobacteria, Chloroflexota, Acidobacteriota, and Actinobacteriota as dominant bacteria. Based on the inorganic nitrogen flux measurements, we identified three types of nitrogen cycling in the sponges: In type 1, sponges (Dendoricella spp. indet., Lissodendoryx cluster) respired aerobically and ammonificated organic matter (OM) to ammonium, fixed N2 to ammonium, and nitrified aerobically heterotrophically produced ammonium to nitrate and nitrite. In type 2, sponges (Halichondria sp., Sceptrulophora, Suberites, Tedania clusters) respired OM aerobically and ammonificated it to ammonium. They also reduced nitrate anaerobically to ammonium via dissimilatory nitrate reduction to ammonium. In type 3, ammonium was microbially nitrified to nitrite and afterwards to nitrate presumably by ammonium-oxidizing Bacteria and/ or Archaea.

ecology↗

bioRxiv2024

Past, present, and future spatial distributions of deep-sea coral and sponge microbiomes revealed by predictive models

Knowledge of the spatial distribution patterns of biodiversity in the ocean is key to evaluate and ensure ocean integrity and resilience. Especially for the deep ocean, where in situ monitoring requires sophisticated instruments and considerable [fi]nancial investments, modelling approaches are crucial to move from scattered data points to predictive continuous maps. Those modelling approaches are commonly run on the macrobial level, but spatio-temporal predictions of host-associated microbiomes are not being targeted. This is especially problematic as previous research has highlighted that host-associated microbes (microbiomes) may display distribution patterns that are not perfectly correlated with host animal biogeographies, but also with other factors such as prevailing environmental conditions. We here establish a new simulation approach and present predicted spatio-temporal distribution patterns of deep-sea sponge and coral microbiomes, making use of a combination of environmental data, host data and microbiome data to advance our understanding of deep-sea microbiomes. This approach allows predictions of microbiome spatio-temporal distribution patterns on scales that are currently not covered by classical sampling approaches at sea. This includes both predictions in space within regional oceanic provinces off eastern North America, and also in time, with predictions into the past and future, covering a time span of 214 years. In summary, our presented predictions allow (i) identi[fi]cation of microbial biodiversity hotspots in the past, present, and future, (ii) evaluation of microbial-macrobial connections at case-study sites through trait-based predictions, and (iii) identi[fi]cation of shifts in microbial community composition (key taxa) across environmental gradients and shifting environmental conditions.

ecology↗

bioRxiv2023

Memory B cells dominate the early antibody-secreting cell response to SARS-CoV-2 mRNA vaccination in naive individuals independently of their antibody affinity

Memory B cells (MBCs) formed over the individuals lifetime constitute nearly half of the adult peripheral blood B cell repertoire in humans. To assess their response to novel antigens, we tracked the origin and followed the differentiation paths of MBCs in the early anti-S response to mRNA vaccination in SARS-CoV-2-naive individuals on single-cell and monoclonal antibody level. Newly generated and pre-existing MBCs differed in their differentiation paths despite similar levels of SARS-CoV-2 and common corona virus S-reactivity. Pre-existing highly mutated MBCs showed no signs of germinal center re-entry and rapidly developed into mature antibody secreting cells (ASCs). In contrast, newly generated MBCs derived from naive precursors showed strong signs of antibody affinity maturation before differentiating into ASCs. Thus, although pre-existing human MBCs have an intrinsic propensity to differentiate into ASCs, the quality of the anti-S antibody and MBC response improved through the clonal selection and affinity maturation of naive precursors. HighlightsO_LImRNA vaccination of SARS-CoV-2 naive individuals recruits naive and pre-existing MBCs with similar levels of S-reactivity into the response C_LIO_LIS-reactive naive but not pre-existing MBCs undergo affinity maturation C_LIO_LIS-reactive pre-existing MBCs dominate the early ASC response independent of their antigen affinity C_LIO_LIHigh-affinity S-reactive MBCs and ASCs develop over time and originate from affinity matured naive precursors C_LI

immunology↗

bioRxiv2023

Spatial connectivity and marine disease dispersal: missing links in aquaculture carrying capacity debates

One major societal challenge is meeting the constantly increasing demand for (sea)food in a sustainable way. With marine aquaculture on the rise, it is crucial to define limits to aquaculture growth in order to ensure ocean health. Along these lines, the concept of aquaculture carrying capacity (CC) is increasingly intersected with the principles of the ecosystem approach to aquaculture. Its primary aims are to estimate sustainable production potential and limits of locally defined regions. However, the ocean is a fluid environment, subject to large- and small-scale dynamics, including ocean currents, tidal fluctuations, and human action. These dynamics introduce spatial connectivity between aquaculture sites and more distant ecosystems than considered in current CC estimates. We argue that far-reaching effects of aquaculture on the ocean, such as introduction and spread of invasive species and marine diseases, are thus underestimated when providing recommendations. Marine diseases can impact biodiversity, society, and overall ocean health and it is imperative to guide aquaculture development to reduce the risk of marine disease dispersal. We, therefore, suggest to embrace spatial ocean connectivity into the CC concept by using hydrodynamic modelling and dispersal simulations as high-throughput methods to estimate potential impact areas and provide risk assessments. In this work, we focus on the example of dispersing infectious diseases in bivalve farming and discuss ecological as well as social consequences of spatial connectivity. Both are applicable to a wide range of organisms and marine aquaculture systems internationally. SummaryThe concept of aquaculture carrying capacity (CC) aims at defining sustainable limits to aquaculture growth in order to ensure ocean health. Usually, estimations are based on locally defined regions and on the farm-scale. However, interactions of aquaculture with the ocean can have far-reaching effects, such as introduction and spread of invasive species and marine diseases. The ocean is a fluid environment, subject to large- and small-scale dynamics that introduce spatial connectivity between aquaculture sites and more distant ecosystems than considered in current CC estimates. We, therefore, suggest to embrace spatial ocean connectivity into the CC concept by using hydrodynamic modelling and dispersal simulations as high-throughput methods to estimate potential impact areas and provide risk assessments. Here, we focus on the example of dispersing infectious diseases in bivalve farming and discuss ecological as well as social consequences of spatial connectivity. Both are applicable to a wide range of organisms and marine aquaculture systems internationally.

systems biology↗

bioRxiv2021

Lower Vibrio spp. abundances in Zostera marina leaf canopies suggest a novel ecosystem function for temperate seagrass beds

Seagrasses, a polyphyletic group of about 60 marine angiosperm species, are the foundation of diverse and functionally important marine habitats along sheltered sedimentary coasts. As a novel ecological function with high societal relevance, a role of the leaf canopy for reducing potentially harmful bacteria has recently been hypothesized. Accordingly, we tested whether or not the abundance of general bacteria and more specifically, those belonging to the genus Vibrio were reduced within temperate Zostera marina (eelgrass) meadows compared to adjacent sand flats and sampled 5 sites in the south-western Baltic Sea using SCUBA. Compared to non-vegetated area, we found an average reduction of 39% for all Vibrio and 63% for the potentially harmful V. vulnificus/cholerae subtype based on robust plate counting data on Vibrio selective agar. The underlying mechanism is currently elusive and clearly merits further study. Our results underline the critical importance of seagrasses in maintaining shallow water ecosystem functioning including water quality and provide further motivation for their protection and restoration.

ecology↗

bioRxiv2020

Hematopoietic stem cells self-renew symmetrically or gradually proceed to differentiation

It is not known whether hematopoietic stem cells (HSCs) undergo symmetric or asymmetric cell divisions in the unperturbed bone marrow. Here, we integrate data from HSC fate mapping and cell-cycle-dependent labeling through mathematical inference and thus gain insight into how HSCs coordinate self-renewal with differentiation. We find that most HSC divisions in adult mice are symmetric self-renewing, replacing HSCs lost by direct differentiation and death, and slowly expanding the HSC population. This expansion maintains constant HSC output to multipotent progenitors (MPPs), despite declining HSC differentiation rate with age. We identify a linear hierarchy of differentiation states between tip HSCs and MPPs, where Tie2-driven HSC fate mapping fully covers the progression of the differentiating cells. A turning point from self-renewal to accelerated cell differentiation occurs between early-stage and late-stage MPPs, just before lineage differentiation becomes manifest in single-cell transcriptomes. This stem cell hierarchy precedes lineage differentiation and may limit mutation accumulation in the hematopoietic system.

systems biology↗

bioRxiv2020

Microbial strategies for survival in the glass sponge Vazella pourtalesii

Few studies have thus far explored the microbiomes of glass sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the glass sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling towards this goal. Microscopic imaging revealed that the host and microbial cells appeared within dense biomass patches that are presumably syncytial tissue aggregates. Based on abundances in amplicon libraries and metagenomic data, SAR324 bacteria, Crenarchaeota, Patescibacteria and Nanoarchaeota were identified as abundant members of the V. pourtalesii microbiome and their genomic potentials were thus analyzed in detail. A general pattern emerged in that the V. pourtalesii symbionts had very small genome sizes in the range of 0.5-2.2 Mb and low GC contents, even below those of seawater relatives. Based on functional analyses of metagenome-assembled genomes (MAGs), we propose two major microbial strategies: the "givers", namely Crenarchaeota and SAR324, heterotrophs and facultative anaerobes, produce and partly secrete all required amino acids and vitamins. The "takers", Nanoarchaeota and Patescibacteria, are anaerobes with reduced genomes that tap into the microbial community for resources, e.g., lipids and DNA, likely using pili-like structures. We posit that the existence of microbial cells in sponge syncytia together with the low-oxygen conditions in the seawater environment are factors that shape the unique compositional and functional properties of the microbial community associated with V. pourtalesii. ImportanceWe investigated the microbial community of V. pourtalesii that forms globally unique, monospecific sponge grounds under low-oxygen conditions on the Scotian Shelf, where it plays a key role for its vulnerable ecosystem. The microbial community was found to be concentrated within biomass patches and is dominated by small cells (<1 m). MAG analyses showed consistently small genome sizes and low GC contents, which is unusual in comparison to known sponge symbionts. These properties as well as the (facultatively) anaerobic metabolism and a high degree of interdependence between the dominant symbionts regarding amino acid and vitamin synthesis are likely adaptations to the unique conditions within the syncytial tissue of their hexactinellid host and the low-oxygen environment.

microbiology↗

bioRxiv2020

GraphGR: A graph neural network to predict the effect of pharmacotherapy on the cancer cell growth

Genomic profiles of cancer cells provide valuable information on genetic alterations in cancer. Several recent studies employed these data to predict the response of cancer cell lines to treatment with drugs. Nonetheless, due to the multifactorial phenotypes and intricate mechanisms of cancer, the accurate prediction of the effect of pharmacotherapy on a specific cell line based on the genetic information alone is problematic. High prediction accuracies reported in the literature likely result from significant overlaps among training, validation, and testing sets, making many predictors inapplicable to new data. To address these issues, we developed GraphGR, a graph neural network with sophisticated attention propagation mechanisms to predict the therapeutic effects of kinase inhibitors across various tumors. Emphasizing on the system-level complexity of cancer, GraphGR integrates multiple heterogeneous data, such as biological networks, genomics, inhibitor profiling, and genedisease associations, into a unified graph structure. In order to construct diverse and information-rich cancer-specific networks, we devised a novel graph reduction protocol based on not only the topological information, but also the biological knowledge. The performance of GraphGR, properly cross-validated at the tissue level, is 0.83 in terms of the area under the receiver operating characteristics, which is notably higher than those measured for other approaches on the same data. Finally, several new predictions are validated against the biomedical literature demonstrating that GraphGR generalizes well to unseen data, i.e. it can predict therapeutic effects across a variety of cancer cell lines and inhibitors. GraphGR is freely available to the academic community at https://github.com/pulimeng/GraphGR.

bioinformatics↗

bioRxiv2020

Microbial diversity of the glass sponge Vazella pourtalesii in response to anthropogenic activities

Establishment of adequate conservation areas represents a challenging but crucial task in the conservation of genetic diversity and biological variability. Anthropogenic pressures on marine ecosystems and organisms are steadily increasing. Whether and to what extent these pressures influence marine genetic biodiversity is only starting to be revealed. Using 16S rRNA gene amplicon sequencing, we analysed the microbial community structure of 33 individuals of the habitat-forming glass sponge Vazella pourtalesii, as well as reference seawater, sediment, and biofilm samples. We assessed how two anthropogenic impacts, i.e. habitat destruction by trawling and artificial substrate provision (moorings made of composite plastic), correspond with in situ V. pourtalesii microbiome variability. In addition, we evaluated the role of two bottom fishery closures in preserving sponge-associated microbial diversity on the Scotian Shelf, Canada. Our results illustrate that V. pourtalesii sponges collected from pristine sites within fishery closures contained distinct and taxonomically largely novel microbial communities. At the trawled site we recorded significant quantitative differences in distinct microbial phyla, such as a reduction in Nitrospinae in sponges and environmental references. Individuals of V. pourtalesii growing on the mooring were significantly enriched in Bacteroidetes, Verrucomicrobia and Cyanobacteria in comparison to sponge individuals growing on the natural seabed. Due to a concomitant enrichment of these taxa in the mooring biofilm, we propose that biofilms on artificial substrates may prime sponge-associated microbial communities when small sponges settle on such substrates. These observations likely have relevant management implications when considering the increase of artificial substrates in the marine environment, e.g., marine litter, off-shore wind parks, and petroleum platforms.

ecology↗

bioRxiv2020

Resolving fate and transcriptome of hematopoietic stem cell clones

Adult bone marrow harbors a mosaic of hematopoietic stem cell (HSC) clones of embryonic origin, and recent work suggests that such clones may have coherent lineage fates. To probe under physiological conditions whether HSC clones with different fates are transcriptionally distinct, we developed PolyloxExpress - a Cre recombinase-dependent DNA substrate for in situ barcoding that allows parallel readout of barcodes and transcriptomes in single cells. We describe differentiation-inactive, multilineage and lineage-restricted HSC clones, find that they reside in distinct regions of the transcriptional landscape of hematopoiesis, and identify corresponding gene signatures. All clone types contain proliferating HSCs, indicating that differentiation-inactive HSCs can undergo symmetric self-renewal. Our work establishes an approach for studying determinants of stem cell fate in vivo and provides molecular evidence for fate coherence of HSC clones.

immunology↗