Changing Ecological Conditions in the Marine Environment Generate Different Microbial Food Web Structures in a Repeatable Manner

The mechanisms responsible for the development of various structural and functional features of the microbial food web (MFW) and their dynamics at spatial and temporal scales, which are important for predicting their responses to future environmental changes, are largely unknown. More than 3000 datasets of environmental and microbial variables collected over a decade on a seasonal and large spatial scale in the Adriatic Sea were analyzed. The sets of environmental variables were classified into four clusters (representing different environmental states) using Neural Gas analysis and the differences in MFW structure between the clusters were analyzed. Different variants of MFW evolve in the different clusters in terms of the abundance of MFW components, their ratios, growth and grazing rates, predator preference in prey selection, the strength of predator-prey interaction, and the relative importance of top-down and bottom-up control. However, these clusters are neither spatially nor temporally fixed; rather, the area studied represents a mosaic of different environmental conditions that alternate from one state to another on a time scale. In each of the environmental states, a distinct structure of MFW develops that shows consistent and repeatable changes that strictly follow the switching in environmental conditions from one state to another.

Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton–bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with ‘mutualistic phytoplankton’—Gammaproteobacteria interactions dominating in the pre-bloom phase and ‘substrate-dependent phytoplankton’—Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics.

Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp.

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48–67, mean about 56 vs. 26–51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

Eco-Biology of Photosynthetic Picoeukaryotes in a Monsoon Influenced Tropical Bay: A Flow Cytometric and Chemotaxonomic Approach

The composition and ecology of photosynthetic picoeukaryotes (PPEUK) are essential for microbial food web functioning. We hypothesize that the simultaneous use of flow cytometry (FCM) and High-Performance-Liquid-Chromatography (HPLC) tools will aid in discerning the dominant PPEUK groups contributing to abundance and biomass under prevailing environmental conditions. The PPEUK seasonal community abundance and pigment biomass were investigated from a south-west monsoon influenced tropical bay from June 2015-May 2016. A size-fractionated (< 3 µm) approach using FCM and HPLC revealed five and six PPEUK groups, respectively. Picocryptophytes dominated the PPEUK biomass under varied environmental conditions, whereas Picodiatoms contributed substantially, being abundant under turbulent, low-temperature, nutrient (NO3−, SiO44−) enriched conditions. The Picochlorophytes dominated the community numerically. The relatively higher abundance and biomass of Picoprasinophytes and a positive correlation with NO3− and NH4+ imply proliferation under higher nutrient concentrations. The least contributors to biomass were Picodinoflagellates and Picoprymnesiophytes. The relatively larger cell size of Picocryptophytes and Picodiatoms resulted in higher cumulative biomass, signifying their role in the microbial food web. Our study proposes incorporation of additional indicator pigments in algorithms used to estimate coastal picophytoplankton contribution to total phytoplankton biomass to avoid discrepancies.

The soil microbial food web revisited: Predatory myxobacteria as keystone taxa?

Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.