Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean

Complex interplay between the microalgae and their microbiome in production raceways

Algae-associated microbiomes are underexplored, limiting our understanding of their influence on the large-scale microalgae reactors. Over two 8-month periods, microbial dynamics were monitored three times per week in two microalgae raceways inoculated with Desmodesmus armatus. One reactor received wastewater, while the other used clean water and fertilizers. The sampled culture volume was filtered into pico and nano size fractions before DNA extraction. Metabarcoding of the 18S and 16S rRNA genes revealed a high microbial diversity across the two time series and a complex eukaryotic and prokaryotic community growing alongside the microalga. Chlorophyta and Fungi were the dominant eukaryotic groups, while Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Bacteroidia dominated the prokaryotic communities. Contrasting Amplicon Sequence Variants (ASVs) were found between healthy (D. armatus abundance > 70 %) and unhealthy (D. armatus abundance 10-20 %) conditions across reactors and time series. Network analysis identified up to 10 potential ecological interactions among D. armatus and its microbiome, predominantly positive. Specific ASVs associated with a healthy condition were positively correlated with D. armatus, while other ASVs linked to an unhealthy condition were negatively correlated. Potentially pathogenic bacteria included Mycobacterium and Flavobacterium, whereas potentially beneficial taxa included Geminocystis, Thiocapsa, Ahniella, and Bosea. Several fungal ASVs showed context-specific associations, whereas specific fungi such as Paraphelidium tribonemae, Aphelidium parallelum, Aphelidium desmodesmi, Aphelidiomycota sp., Rozellomycota sp., and Rhizophidium sp, were identified as potentially harmful. This study reveals the striking diversity and complexity of microalgae-associated microbiomes within raceways, providing valuable insights for optimizing industrial production processes, particularly for wastewater treatment and sustainable green biomass generation.

Evidence of sewage discharge on the coalescence mechanism of aquatic microbial communities during high amplitude hydrological periods

Microbial community coalescence is a ubiquitous ecological process in various ecosystems. However, limited research has addressed the effects of the coalescence on microbial ecological processes and network structure, particularly in the context of sewage discharge during high amplitude hydrological periods. Employing 16S rRNA sequencing and species source tracking analysis, we investigated the coalescence pattern of bacterioplankton in the Chishui river and sewage across various hydrological periods. The results demonstrated that the downstream bacterioplankton mainly originated from the upstream water body, and the sewage discharge from the wastewater treatment plants (WWTPs) had less impact on the downstream bacterioplankton. In the low-water period, the bacterioplankton community showed significant coalescence, and the specialist species and functional taxa gathered in the downstream. Bacterioplankton displayed distinct ecological succession patterns after community coalescence, with notable variations in the abundance of dominant group. Bacterioplankton community assembly was dominated by stochastic processes in river and the sewage over different hydrological periods. The ecological networks exhibited the highest complexity in the high-water period, whereas their stability was most pronounced in the low-water period. Species diversity, as opposed to functional and phylogenetic diversity, might be a more accurate indicator to predict changes in microbial network structure. Our findings will provide new perspectives on the mechanisms of aquatic microbial community coalescence in natural environments.

Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.