Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient

Fungi are an important, but understudied, group of heterotrophic microbes in marine environments. Traditionally, fungi in the coastal ocean were largely assumed to be derived from terrestrial inputs.

RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria

Light is a ubiquitous source of both energy and information in surface environments, and regulates gene expression not only in photosynthetic microorganisms, but in a broad range of photoheterotrophic and heterotrophic microbes as well. Actinobacteria are keystone species in surface freshwater environments, where the ability to sense light could allow them to coordinate periods of nutrient uptake and metabolic activity with primary production. The model freshwater Actinobacteria Rhodoluna (R.) lacicola strain MWH-Ta8 and Aurantimicrobium (A.) photophilum strain MWH-Mo1 grow faster in the light than in the dark, but do not use light energy to support growth. Here, we characterize transcription throughout a light-dark cycle in R. lacicola and A. photophilum. In both species, some genes encoding carbohydrate metabolism and storage are upregulated in the light. However, expression of genes of the TCA cycle is only coordinated with light availability in R. lacicola. In fact, the majority of genes that respond to light and darkness in these two species are different, even though their light-responsive phenotypes are similar. The ability to respond to light and darkness may be widespread in freshwater Actinobacteria, but the genetic networks controlled by these two stimuli may vary significantly.

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.*

BIOCOLONIZATION AND BIODETERIORATION OF MONUMENTS BY CYANOBACTERIA

Cyanobacteria are a morphologically diverse, remarkably adaptable and widely distributed group of photosynthetic prokaryotes, many of which colonize, grow and survive on/in water-limited and nutrient-poor lithic substrates, such as natural rocks/stones and walls of historic monuments and buildings as lithobionts or lithobiontic organisms. They are often the primary colonizers of lithic substrates. They possess protective mechanisms against various abiotic stresses, such as desiccation, high irradiance, high levels of UV-radiation and high temperature which are often encountered on exposed rock surfaces and external walls of lithic monuments and buildings. The biocolonization and growth of cyanobacteria as lithobionts are influenced by various propertiesof monuments, buildings or buildingstones as well as by environmental factors. As photoautotrophs and primary colonizers of lithic substrates, they facilitate and promote the growth and development of heterotrophic microbes, such as bacteria and fungi.The production of extracellular polymeric substances (EPS) leads to the formation of cyanobacteriadominated phototrophic biofilms or sub-aerial biofilms on exposed surfaces of monuments, buildings and rocks/stones. Globally, thebiocolonization, growth and activities of lithobiontic cyanobacteria and other organisms cause unpleasant discoloration, biodeterioration (bioweathering) of monuments and buildings of historical, cultural or religious importance, leading to the aesthetic damage, structural damage and economic loss.These constitute serious problems world-wide. The article provides an overview of the processes of biocolonization and biodeterioration of monuments by lithobiontic(rockinhabiting) cyanobacteria, and their survival as lithobionts.

Housekeeping in the Hydrosphere: Microbial Cooking, Cleaning, and Control under Stress

Who’s cooking, who’s cleaning, and who’s got the remote control within the waters blanketing Earth? Anatomically tiny, numerically dominant microbes are the crucial “homemakers” of the watery household. Phytoplankton’s culinary abilities enable them to create food by absorbing sunlight to fix carbon and release oxygen, making microbial autotrophs top-chefs in the aquatic kitchen. However, they are not the only bioengineers that balance this complex household. Ubiquitous heterotrophic microbes including prokaryotic bacteria and archaea (both “bacteria” henceforth), eukaryotic protists, and viruses, recycle organic matter and make inorganic nutrients available to primary producers. Grazing protists compete with viruses for bacterial biomass, whereas mixotrophic protists produce new organic matter as well as consume microbial biomass. When viruses press remote-control buttons, by modifying host genomes or lysing them, the outcome can reverberate throughout the microbial community and beyond. Despite recognition of the vital role of microbes in biosphere housekeeping, impacts of anthropogenic stressors and climate change on their biodiversity, evolution, and ecological function remain poorly understood. How trillions of the smallest organisms in Earth’s largest ecosystem respond will be hugely consequential. By making the study of ecology personal, the “housekeeping” perspective can provide better insights into changing ecosystem structure and function at all scales.

Species composition and distribution of free-living nematodes in lakes and streams.

This chapter provides an overview of the distributional patterns of nematodes in lakes, rivers, and streams worldwide and of the factors that affect the structuring of nematode communities in the field. Drivers of variability in species composition such as habitat texture, flow rate, temperature, water chemistry, oxygen, vertical distribution of nematodes in the sediment, water depth in lakes, microphytobenthos, macrophytes, heterotrophic microbes, interspecific competition, and predation, are discussed.

Developing a microbial consortium for removing nutrients in dishwasher wastewater: towards a biofilter for its up-cycling

Microbial consortia are effective biofilters to treat wastewaters, allowing for resource recovery and water remediation. To reuse and save water in the domestic cycle, we assembled a suspended biofilm, a ‘biofilter’ to treat dishwasher wastewater. Bacterial monocultures of both photo- and heterotrophs were assembled in an increasingly complex fashion to test their nutrient stripping capacity. This ‘biofilter’ is the core of an integrated system (Zero Mile System) devoted to reusing and upcycling of reconditioned wastewater, partly in subsequent dishwasher cycles and partly into a vertical garden for plant food cultivation. The biofilter was assembled based on a strain of the photosynthetic, filamentous cyanobacterium Trichormus variabilis, selected to produce an oxygen evolving scaffold, and three heterotrophic aerobic bacterial isolates coming from the dishwasher wastewater itself: Acinetobacter, Exiguobacterium and Pseudomonas spp. The consortium was constructed starting with 16 isolates tested one-to-one with T. variabilis and then selecting the heterotrophic microbes up to a final one-to-three consortium, which included two dominant and a rare component of the wastewater community. This consortium thrives in the wastewater much better than T. variabilis alone, efficiently stripping N and P in short time, a pivotal step for the reuse and saving of water in household appliances.