A robust approach to estimate relative phytoplankton cell abundances from metagenomes

From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance

Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

The impact of flooding from the Minjiang River on the succession of harmful algal blooms (HABs) caused by diatoms in China's offshore waters

This study examines diatom assemblages in the Matsu Archipelago, an area influenced by Minjiang River runoff. It focuses on harmful algal blooms (HABs) that occurred between August 2021 and July 2022. Utilizing 18S rRNA metabarcoding and microscopic analysis, we observed a significant diatom bloom during early summer runoff, peaking at 5 × 105 cells L-1. The research reveals dynamic community changes during the runoff season, with dominant genera including Pseudo-nitzschia, Chaetoceros, and Skeletonema. Skeletonema cell density correlated with NO3 levels, Chaetoceros had a slight PO4 affinity, and Pseudo-nitzschia showed a negative correlation with Skeletonema. Pseudo-nitzschia, which prefers high light and pH conditions, had notably high concentrations in the flood season and in the autumn. In both, it was dominated by potential toxin-producing species - P. multistriata and P. pungens during the flooding, and P. cuspidate in the autumn. These findings highlight the intricate relationship between diatom dynamics and environmental factors, providing essential insights for managing HABs, especially Pseudo-nitzschia species, amidst environmental changes.

Prevalence and Preferred Niche of Small Eukaryotes with Mixotrophic Potentials in the Global Ocean

Unicellular eukaryotes that are capable of phago-mixotrophy in the ocean compete for inorganic nutrients and light with autotrophs, and for bacterial prey with heterotrophs. In this study, we ask what the overall prevalence of eukaryotic mixotrophs in the vast open ocean is, and how the availability of inorganic nutrients, light, and prey affects their relative success. We utilized the Tara Oceans eukaryotic 18S rRNA gene and environmental context variables dataset to conduct a large-scale field analysis. We also performed isolate-based culture experiments to verify growth and nutritional resource relationships for representative mixotrophic taxa. The field analysis suggested that the overall prevalence of mixotrophs were negatively correlated with nutrient concentrations and positively associated with light availability. Concentrations of heterotrophic bacteria as a single variable also presented a positive correlation with mixotrophic prevalence, but to a lesser extent. On the other hand, the culture experiments demonstrated a taxa-specific relationship between mixotrophic growth and nutrition resources, i.e., the growth of one group was significantly dependent on light availability, while the other group was less affected by light when they received sufficient prey. Both groups were capable of growing efficiently with low inorganic nutrients when receiving sufficient prey and light. Therefore, our field analysis and culture experiments both suggest that phago-mixotrophy for ocean eukaryotes is seemingly an efficient strategy to compensate for nutrient deficiency but unnecessary to compensate for light scarcity. This study collectively revealed a close relationship between abiotic and biotic nutritional resources and the prevalence of trophic strategies, shedding light on the importance of light and nutrients for determining the competitive success of mixotrophs versus autotrophic and heterotrophic eukaryotes in the ocean.

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters

Community and diversity shifts of bacteria and microeukaryotes with strong environmental and spatial variations have been unveiled in the Pearl River Estuary (PRE) and northern coastal part of South China Sea (SCS). However, it is not clear what the determining factors shape the microbial community and how the biotic interactions respond to the estuarine and oceanic environment. Here, we established the multiple regression models (MRM) and co-occurrence networks on microbial communities in PRE and SCS habitats. The results showed that there were significant differences of the abiotic factors affecting the bacterial and microeukaryotic communities between PRE and SCS habitats. Salinity explained the largest variations to the microbial community dissimilarities in PRE. Whereas spatial and environmental factors determined the microbial community dissimilarities in SCS. Positive relations between parasitic lineages (e.g. Perkinsea and Cercozoa) and algal taxa (Dinophyceae, Cryptophyta, Chlorophyta and Ochrophyta) dominated in the PRE network. While parasites Syndiniales positively correlated with other Syndiniales and protists in SCS. Strong positive associations among autotrophic and heterotrophic groups were revealed in both niches. Therefore, the biotic interactions are also important and may be responsible for the unexplained variations of the abiotic factors from MRM models. Microbial network in the PRE estuarine water had weakened resistance to environmental disturbances, while the SCS network had greater capacity to maintain network stability. This study shed light on the different mechanisms of abiotic and biotic factors in shaping the compositions of bacteria and microeukaryotes between PRE and SCS niches, and highlights the weakening effect of environmental disturbances on the microbial network stability.

Domain-level Identification of Single Prokaryotic Cells by Optical Photothermal Infrared Spectroscopy

Infrared spectroscopy is used for the chemical characterization of prokaryotes. However, its application has been limited to cell aggregates and lipid extracts because of the relatively low spatial resolution of diffraction. We herein report optical photothermal infrared (O-PTIR) spectroscopy of prokaryotes for a domain-level diagnosis at the single-cell level. The technique provided infrared spectra of individual bacterial as well as archaeal cells, and the resulting aliphatic CH3/CH2 intensity ratios showed domain-specific signatures, which may reflect distinctive cellular lipid compositions; however, there was interference by other cellular components. These results suggest the potential of O-PTIR for a domain-level diagnosis of single prokaryotic cells in natural environments.