Evaluation of the Production of Dissolved Organic Matter by Three Marine Bacterial Strains

Bottom-up and top-down controls on Alteromonas macleodii lead to different dissolved organic matter compositions

The effects of both bottom-up (e.g. substrate) and top-down (e.g. viral lysis) controls on the molecular composition of dissolved organic matter have not been investigated. In this study, we investigated the dissolved organic matter composition of the model bacterium Alteromonas macleodii ATCC 27126 growing on different substrates (glucose, laminarin, extracts from a Synechococcus culture, oligotrophic seawater, and eutrophic seawater), and infected with a lytic phage. The ultra-high resolution mass spectrometry analysis showed that when growing on different substrates Alteromonas macleodii preferred to use reduced, saturated nitrogen-containing molecules (i.e. O4 formula species) and released or preserved oxidized, unsaturated sulfur-containing molecules (i.e. O7 formula species). However, when infected with the lytic phage, Alteromonas macleodii produced organic molecules with higher hydrogen saturation, and more nitrogen- or sulfur-containing molecules. Our results demonstrate that bottom-up (i.e. varying substrates) and top-down (i.e. viral lysis) controls leave different molecular fingerprints in the produced dissolved organic matter.

Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions

The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO₂, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.

A case study: The deployment of a novel in situ fluorimeter for monitoring biological contamination within the urban surface waters of Kolkata, India

The quality and health of many of our vital freshwater systems are poor. To tackle this with ever increasing pressures from anthropogenic and climatic changes, we must improve water quality monitoring and devise and implement more appropriate water quality parameters. Recent research has highlighted the potential for Peak T fluorescence (tryptophan-like fluorescence, TLF) to monitor microbial activity in aquatic systems. The VLux TPro (Chelsea Technologies Ltd., UK), an in situ real-time fluorimeter, was deployed in different urban freshwater bodies within Kolkata (West Bengal, India) during March 2019. This study is the first to apply this technology in surface waters within a densely populated urban area. Spot-sampling was also undertaken at 13 sampling locations enabling physicochemical analysis, bacterial enumeration and determination of nutrient (nitrate and phosphate) concentrations. This case study has demonstrated the ability of an in situ fluorimeter, VLux TPro, to successfully identify both biological contamination events and potential elevated microbial activity, related to nutrient loading, in complex surface freshwaters, without the need for expensive and time-consuming laboratory analysis.

Bacterial Transformation and Processing of Diatom-Derived Organic Matter: A Case Study for Skeletonema dohrnii

Bacterial transformation and processing of phytoplankton-derived organic matter are extremely important for the formation of ubiquitous organic matter (OM) in aquatic ecosystems. Heterotrophic bacteria convert OM into biomass and recycle inorganic components, contributing to the production of microbial food webs. While phytoplankton-derived organic matter is commonly studied, the transformation and processing of dissolved OM (DOM) and lysate OM (LOM) by culturable epiphytic bacteria remains poorly understood. In this study, cultivable epiphytic bacteria from the marine diatom, Skeletonema dohrnii, were isolated, purified, and identified. Three bacteria, Roseobacteria sp., Marinobacter sp., and Bacillus sp., were selected to study the transformation and processing of S. dohrnii-derived DOM and LOM using excitation-emission matrix (EEM) fluorescence methods, and bacterial abundance, dissolved organic carbon (DOC) concentration, and transparent exopolymer particle (TEP) content were measured. Meanwhile, the bacterial transformation of DOM and LOM was further evaluated by the fluorescence index, biological index, β/α, and humification index. The primary fluorophores, peak A (humic-like), peak C (humic-like), peak M (humic-like), peak B (protein-like), and peak T (tryptophan-like), were present in the sample. The fluorescence of DOM and LOM was dominated by protein-like signal that became increasingly humic-like over time, suggesting that more complex molecules (e.g., recalcitrant OM) are being produced. The fluorescence of DOM and LOM was dominated by a protein-like signal that became increasingly humic-like over time, suggesting that epiphytic bacteria produced more complex molecules. Results showed that the bacteria utilized LOM more rapidly than DOM. While the three bacteria transformed OM to different degrees, all were able to facilitate microbial reprocessing of OM into refractory OM.

Characteristics of Chromophoric Dissolved Organic Matter (CDOM) Produced by Heterotrophic Bacteria Isolated from Aquaculture Systems

Heterotrophic bacteria (HB) play an important role in aquatic ecosystems as recyclers of dissolved organic matter (DOM). The objective of this study was to characterize the spectral characteristics of intracellular (IC), and extracellular (EC) compounds produced by 12 HB isolated from two aquaculture systems. Microorganisms belonging to the genera Bacillus, Paenibacillus, and Psychrobacillus were identified by analysis of the 16S ribosomal gene. Aliquots of bacterial culture were centrifugated every hour (1st to 7th) to obtain the EC compounds. The pellet was ultrasound-lysed to obtain the IC compounds. Excitation-emission matrices were used in combination with parallel factor analysis (PARAFAC) to characterize the fluorescent components of DOM (FDOM). PARAFAC indicated two protein-like components and two humic-like components in both cell spaces. At the IC, B. macquariensis showed a high fluorescence index (FI), probably associated with fulvic acid, quinones, or ketones. Psychrobacillus insolitus showed an inverse correlation between spectral slopes S275–295 and S350–400 in the EC and IC fractions, which may indicate differential release of low and high molecular weight molecules in these two fractions. The opposite occurred with B. licheniformis and P. alvei. The origin of FDOM in HB is an important finding of this work. The most significant amount of protein-like substances was produced at the IC level, with the humic- and fulvic-type at the EC. The main finding of this work is the evidence of differential production of humic-type or protein-type FDOM production by HB species from marine and freshwater aquaculture systems in their intracellular and extracellular fractions, as well different relative molecular weight. For aquaculture, these findings suggest that some bacterial species show promise in supplying essential amino acids to growing organisms, and others play a major role in nutrient exchange and the global carbon cycle.

Transformations of Diatom-Derived Dissolved Organic Matter by Bacillus pumilus Under Warming and Acidification Conditions

Heterotrophic bacteria are assumed to play an important role in processing of phytoplankton-derived dissolved organic matter (DOM). Although the algae-derived organic matter is commonly studied, the transformation and processing of DOM by epiphytic bacteria for phytoplankton have rarely been investigated, especially under warming and acidification. In this study, Bacillus pumilus is used to explore the ecologically important marine diatom Skeletonema dohrnii-derived DOM under different conditions (temperature, 27°C and 31°C; pCO2, 400 and 1,000 ppm), utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC). Fluorescence regional integration and the peak selecting method are used to generate B, T, N, A, M, and C peaks in the EEM fluorescence spectroscopy. The main known fluorophores including that protein-like components (peaks B and T), unknown components (peak N), and humic-like component (peaks A, M, and C). Our experimental results showed that under higher temperature and pressure of CO2 (pCO2) conditions, S. dohrnii-derived DOM fluorescence was dominated by a protein-like signal that slower waning throughout the experiment, becoming an increasingly humic-like substance, implying that processing by the epiphytic bacteria (B. pumilus) produced more complex molecules. In addition, spectroscopic indices (e.g., fluorescence index, biological index, freshness index β/α, and humification index) were changed in varying degrees. This study reveals and confirms the direct participation of heterotrophic bacteria in the transformation and generation of algae-derived DOM in the laboratory, underlining the influence of global warming and ocean acidification on this process.

Laboratory In-Situ Production of Autochthonous and Allochthonous Fluorescent Organic Matter by Freshwater Bacteria

This work investigates the origin and range of fluorescent organic matter (FOM) produced in-situ by environmentally sourced freshwater bacteria. Aquatic FOM is an essential component in global carbon cycling and is generally classified as either autochthonous, produced in-situ via microbial processes, or allochthonous, transported into aquatic systems from external sources. We have demonstrated that, within laboratory model systems, environmentally sourced mixed microbial communities and bacterial isolates can produce and/or export FOM associated with both autochthonous and allochthonous material. This study focuses on fluorescence peak B, T, M, C and C+, exploring (1) the cellular nature of FOM produced, (2) FOM exported as extracellular material into the water column and (3) the impact of physical cell lysis on FOM signature. For the laboratory model systems studied, Peak T fluorescence is retained within bacterial cells (>68%), while Peak C fluorescence is mainly observed as extracellular material (>80%). Peak M is identified as both cellular and extracellular FOM, produced by all isolated freshwater microorganisms investigated. The origin of Peak C+ is postulated to originate from functional metabolites associated with specific microorganisms, seen specifically within the Pseudomonas sp. monoculture here. This work challenges the binary classification of FOM as either allochthonous or autochthonous, suggesting that FOM processing and production occurs along a dynamic continuum. Within this study, fluorescence intensity data for the environmental bacteria isolate monocultures are presented as enumeration corrected data, for the first time providing quantitative fluorescence data per bacterial colony forming unit (cfu). From this, we are able to assess the relative contribution of different bacteria to the autochthonous FOM pool and if this material is cellular or extracellular.