Gut Microbiome Alteration of Cold-adapated Antarctic copepod Tigriopus kingsejongensis with Temperature Changes and Developmental Stages

Tigriopus kingsejongensis, a copepod species, reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. Some copepods were temperature-sensitive in growth and post-embryonic development. We cultured T. kingsejongensis at three different temperatures (2°C, 8°C, and 15°C) in a laboratory to observe the alterations in the stool microbiome of copepods depending on the cultivation temperature and developmental stages. We observed copepod gut microbiome changes by increasing temperatures: a lower microbial diversity, a higher abundance of aquatic microbes, Vibrio, and a lower abundance of the psychrophilic microbes, Colwellia. Also, the copepod gut microbiome, according to the developmental stage, was changed: a lower microbial diversity in egg-attached copepods than nauplius at 8°C. We further analyzed three shotgun metagenomes from T. kingsejongensis stool samples at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolase (GHs) encoding chitinases and virulence factors with higher relative abundance at 15°C than at lower temperatures. These results that temperature and developmental stages affect the gut microbiome of copepods are helpful to understand the changes in the low-temperature adapted copepod with climate change.

The Vibrio cholerae T6SS is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae , an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was essential for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.

Vibrio cholerae Infection Induces Strain Specific Modulation of the Zebrafish Intestinal Microbiome

Zebrafish ( Danio rerio ) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core ( i.e. , consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae . As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae in order for colonization, and subsequent disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few have examined how a V. cholerae infection alters the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was utilized to investigate how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and specific microbes that are targeted depend on the V. cholerae genotype.

Ocean currents promote rare species diversity in protists

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protist species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that chaotic advection by oceanic currents affects biodiversity patterns of rare species. To test this hypothesis, we introduce a spatially explicit coalescence model that reconstructs the species diversity of a sample of water. Our model predicts, in the presence of chaotic advection, a steeper power law decay of the species abundance distribution and a steeper increase of the number of observed species with sample size. A comparison of metagenomic studies of planktonic protist communities in oceans and in lakes quantitatively confirms our prediction. Our results support that oceanic currents positively affect the diversity of rare aquatic microbes.

Effects of Vibrio cholerae infection and colonization on the zebrafish intestinal microbiome

Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic, and can be significantly altered to due external factors. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae needs to colonize the intestine of an exposed host for any type of pathogenicity to occur. It is suspected that members of the resident intestinal microbial community need to be eliminated by V. cholerae in order for colonization, and subsequently disease, to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal community. In this study, 16S rRNA gene sequencing was utilized to investigate how various strains of V. cholerae alter the aforementioned microbial profiles following an infection. We found that V. cholerae infection and subsequent colonization induced significant changes in the zebrafish intestinal microbiome, with specific members of the microbial community targeted. Additional salient differences to the microbial profile were observed based on the particular strain of V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae causes significant modulation to the zebrafish intestinal microbiome in order for infection and subsequent disease to occur.

An experimental test of the capacity for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage

Waterfowl are potential long-distance dispersal vectors for aquatic microbes such as diatoms, but experimental evidence is scarce. We conducted an experiment designed to emulate diatom dispersal via adherence to waterfowl, and to evaluate the effects of humidity and transport duration on potential dispersal success. We dipped individual mallard breast feathers in a pure benthic diatom culture (Nitzschia pusilla Grunow), then subjected them to one of four relative humidity levels (RH; from ca. 8% to 88%) crossed with one of four transport durations (10, 60, 120, 240 minutes) within a chamber through which air was passed continuously, mimicking light wind. We then placed the feather on sterile growth medium. After two weeks we used spectrofluorometry to detect diatom growth and thus diatom viability. A logistic regression on viability revealed a significant interaction between transport duration and RH: the negative effect of duration was strongest under lower RH conditions, but under high RH (88%) the probability of being viable was moderate to high regardless of transport duration. Importantly, even after 4 hours, the probability of being viable was predicted to be 0.45 (95% confidence interval: 0.18 to 0.75). We then placed our findings in the geographic context of the central waterfowl migration flyway in North America, and specifically Nebraska, South Dakota, and North Dakota, for which sufficient data were available to enable geospatial predictions of potential mallard-borne diatom dispersal. Combined with published data about (i) mallard flight speeds, (ii) the geographic distribution of surface waters and of N. pusilla, and (iii) daytime RH during the months of April through June, our model predicted high probabilities of potential dispersal among the region’s suitable water bodies.

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

ABSTRACT The SAR11 clade is one of the most abundant bacterioplankton groups in surface waters of most of the oceans and lakes. However, only 15 SAR11 phages have been isolated thus far, and only one of them belongs to the Myoviridae family (pelagimyophages). Here, we have analyzed 26 sequences of myophages that putatively infect the SAR11 clade. They have been retrieved by mining ca. 45 Gbp aquatic assembled cellular metagenomes and viromes. Most of the myophages were obtained from the cellular fraction (0.2 μm), indicating a bias against this type of virus in viromes. We have found the first myophages that putatively infect Candidatus Fonsibacter (freshwater SAR11) and another group putatively infecting bathypelagic SAR11 phylogroup Ic. The genomes have similar sizes and maintain overall synteny in spite of low average nucleotide identity values, revealing high similarity to marine cyanomyophages. Pelagimyophages recruited metagenomic reads widely from several locations but always much more from cellular metagenomes than from viromes, opposite to what happens with pelagipodophages. Comparing the genomes resulted in the identification of a hypervariable island that is related to host recognition. Interestingly, some genes in these islands could be related to host cell wall synthesis and coinfection avoidance. A cluster of curli-related proteins was widespread among the genomes, although its function is unclear. IMPORTANCE SAR11 clade members are among the most abundant bacteria on Earth. Their study is complicated by their great diversity and difficulties in being grown and manipulated in the laboratory. On the other hand, and due to their extraordinary abundance, metagenomic data sets provide enormous richness of information about these microbes. Given the major role played by phages in the lifestyle and evolution of prokaryotic cells, the contribution of several new bacteriophage genomes preying on this clade opens windows into the infection strategies and life cycle of its viruses. Such strategies could provide models of attack of large-genome phages preying on streamlined aquatic microbes.

Ocean currents promote rare species diversity in protists

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protists species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that oceanic currents affect biodiversity patterns of rare species. To test this hypothesis, we introduce a spatially-explicit coalescence model able to reconstruct the species diversity in a sample of water. Our model predicts, in the presence of oceanic currents, a steeper power law decay of the species abundance distribution and a steeper increase of the number of observed species with sample size. A comparison of two metagenomic studies of planktonic protist communities in oceans and in lakes quantitatively confirms our prediction. Our results support that oceanic currents positively impact the diversity of rare aquatic microbes.

Evolution in action: Habitat-transition leads to genome-streamlining in Methylophilaceae (Betaproteobacteriales)

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (‘Ca. Methylopumilus’) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteriales), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or are encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome-reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome-streamlining as such a collection of evolutionarily related microbes from different habitats is practically unknown for other similarly abundant microbes (e.g., ‘Ca. Pelagibacterales’, ‘Ca. Nanopelagicales’).

Ultrafast excited state dynamics of nonfluorescent cyclopheophorbide-aenol, a catabolite of chlorophyll-adetoxified in algae-feeding aquatic microbes

Transient absorption spectroscopy revealed that a catabolite of chlorophyll-a, cPPB-aE, undergoes ultrafast nonradiative decay through an intermediate state.