Biology subjects

Herndl, G. J.

Publications and source records attributed to Herndl, G. J..

9 recordsLinked to original sources

bioRxiv2025

Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean

Prokaryotes play a central role in marine biogeochemical cycles, yet quantifying their activity requires sensitive methods due to low biomass and metabolic rates, particularly in the deep ocean. One recent method to determine single-cell activity of prokaryotes is bioorthogonal non-canonical amino acid tagging (BONCAT), which offers a non-radioactive approach to measure protein synthesis. However, direct comparisons between BONCAT and radioisotope-based techniques across ocean depth gradients remain limited, particularly for low-activity prokaryotic communities. To address this knowledge gap, we tested an optimised BONCAT protocol using picolyl azide fluorophores (BONCAT-pic) to assess single-cell heterotrophic activity in prokaryotic communities from surface to bathypelagic depths (1000-4000 m) in the Southern Ocean near the Kerguelen Islands. The method was first optimised using aged coastal and open-ocean seawater, and then compared to microautoradiography with 3H-methionine uptake. Statistical analysis shows that BONCAT-pic significantly improved detection sensitivity compared to standard azide reagents. BONCAT-pic consistently detected active cells in profiles over the open ocean water column, with cell proportions and fluorescence signals closely correlating with both microautoradiography (R2 = 0.9, p < 0.001) and bulk methionine incorporation (R2 = 0.6, p < 0.001). Our results demonstrate that BONCAT-pic is a reliable, fluorescence-based method for quantifying heterotrophic activity at the single-cell level, extending its applicability to prokaryotic communities in the deep ocean.

microbiology↗

bioRxiv2025

Distinct functional potential of bacterial extracellular vesicles across biogeographic provinces of the South Pacific Ocean

Bacterial extracellular vesicles (BEVs) are nanoscale membranous structures released by diverse types of bacteria. Laboratory model systems indicate that these nanoparticles may play several roles in the ecophysiology of marine bacteria. However, their actual functionality in the environment remains unclear. Here we describe the proteomic composition of marine BEVs over more than 5,000 nautical miles of surface waters in the South Pacific, linking BEV cargoes to the bacterial communities producing them. BEVs were consistently present across a range of biogeochemical conditions, with an overall abundance comparable to that of bacterial cells. However, the protein content of the BEVs varied significantly between different ocean regions. The BEVs were enriched in carbohydrate transporters under phytoplankton bloom conditions, and contained iron and phosphate uptake-related proteins in nutrient-limited waters. This suggests that BEVs could enable cells to perform key extracellular functions in the marine environment. Our observations further highlight the prevalence of BEVs and the biogeographic patterns of their functional potential across oceanic scales.

microbiology↗

bioRxiv2024

Jellyfish blooms - an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments

Jellyfish, and gelatinous zooplankton (GZ) in general, represent an important component of marine food webs. Certain GZ species are capable of generating massive blooms of severe environmental impact. These blooms are often followed by a sudden collapse of the entire population, introducing considerable amounts of organic matter (GZ-OM) in the oceans interior. GZ-OM represents an abundant substrate to promote bacterial growth and copious colonizable surface for microbial interactions. Hence we hypothesized that this GZ-OM serves as a yet overlooked hotspot for transmitting antimicrobial resistance genes (ARGs) in marine environments. For this we experimentally evolved and analyzed marine microbial communities in microcosms in presence and absence of OM from scyphozoan Aurelia aurita s.l. and ctenophore Mnemiopsis leidyi. Communities evolved under GZ-OM exposure displayed an up to 4-fold increase in relative ARG and an up to 10-fold increase in abundance of horizontally transferable mobile genetic elements (MGEs) per 16S rRNA gene copy compared to the controls. This trait was consistent across ARG and MGE classes and independent of the GZ species, suggesting that the underlying mechanism is indeed based on the general influx of nutrients and colonizable surfaces. Potential ARG carriers included known key GZ-OM degraders, but also genera containing potential pathogens hinting towards an increased risk of ARG transfer to pathogenic strains. Here, Vibrio were pinpointed as potential key species directly associated with several significantly elevated ARGs and MGEs. Subsequent whole-genome sequencing of a Vibrio isolate from the microcosm experiment revealed the genetic potential for the mobilization and transfer of ARGs in GZ-OM degrading microbial consortia. With this study, we established the first link between two emerging issues of marine coastal zones, jellyfish blooms and AMR spread, both likely increasing in projected future ocean scenarios.

microbiology↗

bioRxiv2023

Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter

Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. Compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation revealed that, despite the fundamental genetic and biochemical differences between the two species, a similar pattern in the bacterial community response was observed. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic exoenzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study. Taken together our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM. ImportanceJellyfish blooms are increasingly becoming a recurring seasonal event in marine ecosystems, characterised by a rapid build-up of gelatinous biomass that collapses rapidly. Although these blooms have the potential to cause major perturbations, their impact on marine microbial communities is largely unknown. We conducted an incubation experiment simulating a bloom of the ctenophore Mnemiopsis leidyi in the Northern Adriatic, where we investigated the bacterial response to the gelatinous biomass. We found that the bacterial communities actively degraded the gelatinous organic matter, and overall showed a striking similarity to the dynamics previously observed after a simulated bloom of the jellyfish Aurelia aurita s.l. In both cases we found that a single bacterial species, Pseudoalteromonas phenolica, was responsible for most of the degradation activity. This suggests that blooms of different jellyfish are likely to trigger a consistent response from natural bacterial communities, with specific bacterial species driving the remineralisation of gelatinous biomass.

microbiology↗

bioRxiv2022

Characterization of membrane vesicles in Alteromonas macleodii indicates potential roles in their copiotrophic lifestyle

Bacterial membrane vesicles (MVs) are likely abundant in the oceans. Based on observations from non-marine bacteria, MVs are involved in a range of physiological processes and play important roles in interactions between microbial cells. In this study we characterized MV production of six different strains of Alteromonas macleodii, a cosmopolitan marine bacterium. A. macleodii strains produced MVs at rates of up to 30 MVs cell-1 generation-1. The produced MVs had high morphological diversity that could potentially define their functional roles. Proteomic characterization revealed that MVs are rich in membrane proteins related to iron and phosphate uptake, as well as proteins with potential functions in biofilm formation. Furthermore, MVs were harboring hydrolytic enzymes. Taken together, our results suggest that in the largely oligotrophic oceans, A. macleodii MVs may support its growth through generation of extracellular "hotspots" that facilitate access to essential substrates. This study provides an important basis for further investigation of the ecological relevance of MVs in heterotrophic marine bacteria.

microbiology↗

bioRxiv2022

Impact of hydrostatic pressure on organic carbon cycling of the deep-sea microbiome

Deep-sea microbial communities are exposed to high hydrostatic pressure. While some of these deep-sea prokaryotes are adapted to high-pressure conditions, the contribution of piezophilic (i.e., pressure-loving) and piezotolerant prokaryotes to the total deep-sea prokaryotic community remains unknown. Here we show that the metabolic activity of prokaryotic communities is increasingly inhibited with increasing hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was only about one-third of that measured on the same community at atmospheric pressure conditions. Only [~]5% of the bathypelagic prokaryotic community are piezophilic while [~]85% of the deep-sea prokaryotes are piezotolerant. A small fraction ([~]10%) of the deep-sea prokaryotes is piezosensitive (mainly members of Bacteroidetes, Alteromonas) exhibiting specific survival strategies at meso- and bathypelagic depths. These piezosensitive bacteria elevated their activity by more than 100-fold upon depressurization. Hence, the consistently higher bulk metabolic activity of the deep-sea prokaryotic community measured upon depressurization is due to a rather small fraction of the prokaryotic community. Overall, the heterotrophic prokaryotic activity in the deep-sea is substantially lower than hitherto assumed with major impacts on the oceanic carbon cycling.

ecology↗

bioRxiv2021

Microbial consortiums of putative degraders of low-density polyethylene-associated compounds in the ocean

Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analysed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for two years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harboured genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This study identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential of utilizing LDPE-associated compounds as carbon and energy source. ImportanceLow-density polyethylene (LDPE) is one of the most used plastics worldwide and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After two years of incubation, two of the microbial communities exhibited a very similar taxonomic composition mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean, that might have the potential to degrade LDPE-associated compounds, and that alkane degradation pathways might be involved.

microbiology↗

bioRxiv2021

Limited accessibility of nitrogen supplied as amino acids, amides, and amines as energy sources for marine Thaumarchaeota

Genomic and physiological evidence from some strains of ammonia-oxidizing Thaumarchaeota demonstrate their additional ability to oxidize nitrogen (N) supplied as urea or cyanate, fueling conjecture about their ability to conserve energy by directly oxidizing reduced N from other dissolved organic nitrogen (DON) compounds. Similarly, field studies have shown rapid oxidation of polyamine-N in the ocean, but it is unclear whether Thaumarchaeota oxidize polyamine-N directly or whether heterotrophic DON remineralization is required. We tested growth of two marine Nitrosopumilus isolates on DON compounds including polyamines, amino acids, primary amines, and amides as their sole energy source. Though axenic cultures only consumed N supplied as ammonium or urea, there was rapid but inconsistent oxidation of N from the polyamine putrescine when cultures included a heterotrophic bacterium. Surprisingly, axenic cultures oxidized 15N-putrescine during growth on ammonia, suggesting co-metabolism or accelerated breakdown of putrescine by reactive metabolic byproducts. Nitric oxide, hydrogen peroxide, or peroxynitrite did not oxidize putrescine in sterile seawater. These data suggest that the N in common DON molecules is not directly accessible to marine Thaumarchaeota, with thaumarchaeal oxidation (and presumably assimilation) of DON-N requiring initial heterotrophic remineralization. However, reactive byproducts or enzymatic co-metabolism may facilitate limited thaumarchaeal DON-N oxidation.

microbiology↗

bioRxiv2019

Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean

Ammonia-oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20-40% of the oceans prokaryotic plankton and thus play an important role in global nitrogen cycle. However, it remains enigmatic to what extent these chemolithoautotrophic archaea are releasing dissolved organic matter (DOM). A combination of targeted and untargeted metabolomics was used to characterise the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Furthermore, we compared the composition of intra- and extracellular dissolved free amino acids (DFAA). Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivity, dominated by nitrogen-containing compounds. A significant fraction of the released DOM consisted of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. In growing Nitrosopumilus cultures, hydrophobic amino acids were likely released as a result of passive diffusion corresponding to ammonia oxidation activity, while glycine was continuously released at high rates. Our results suggest that AOA release several ecologically and biochemically relevant metabolites, potentially fueling heterotrophic prokaryotes in the ocean.

ecology↗