Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead‐end

Caves are perceived as isolated, extreme habitats with a uniquely specialized biota, which long ago led to the idea that caves are “evolutionary dead‐ends.” This implies that cave‐adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independently evolved cave‐dwelling groups. Here, we use the freshwater crayfish, a group with dozens of cave‐dwelling species in multiple lineages, as a system to test this hypothesis. We consider historical patterns of lineage diversification and habitat transition as well as current patterns of geographic range size. We find that while cave‐dwelling lineages have small relative range sizes and rarely transition back to the surface, they exhibit remarkably similar diversification patterns to those of other habitat types and appear to be able to maintain a diversity of lineages through time. This suggests that cave adaptation is not a “dead‐end” for freshwater crayfish, which has positive implications for our understanding of biodiversity and conservation in cave habitats.     

In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM¹²) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM¹² interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM¹² interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.Subject terms: Microbiome, Microbial ecology     

Life-Style and Genome Structure of Marine Pseudoalteromonas Siphovirus B8b Isolated from the Northwestern Mediterranean Sea

Marine viruses (phages) alter bacterial diversity and evolution with impacts on marine biogeochemical cycles, and yet few well-developed model systems limit opportunities for hypothesis testing. Here we isolate phage B8b from the Mediterranean Sea using Pseudoalteromonas sp. QC-44 as a host and characterize it using myriad techniques. Morphologically, phage B8b was classified as a member of the Siphoviridae family. One-step growth analyses showed that this siphovirus had a latent period of 70 min and released 172 new viral particles per cell. Host range analysis against 89 bacterial host strains revealed that phage B8b infected 3 Pseudoalteromonas strains (52 tested, >99.9% 16S rRNA gene nucleotide identity) and 1 non-Pseudoaltermonas strain belonging to Alteromonas sp. (37 strains from 6 genera tested), which helps bound the phylogenetic distance possible in a phage-mediated horizontal gene transfer event. The Pseudoalteromonas phage B8b genome size was 42.7 kb, with clear structural and replication modules where the former were delineated leveraging identification of 16 structural genes by virion structural proteomics, only 4 of which had any similarity to known structural proteins. In nature, this phage was common in coastal marine environments in both photic and aphotic layers (found in 26.5% of available viral metagenomes), but not abundant in any sample (average per sample abundance was 0.65% of the reads). Together these data improve our understanding of siphoviruses in nature, and provide foundational information for a new ‘rare virosphere’ phage–host model system.     

Changes in biooxidation mechanism and transient biofilm characteristics by As(V) during arsenopyrite colonization with <Emphasis Type="Italic">Acidithiobacillus thiooxidans</Emphasis>

Chemical and surface analyses are carried out using Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM–EDS), atomic force microscopy (AFM), confocal laser scanning microscopy (CLSM), glow discharge spectroscopy (GDS) and extracellular surface protein quantification to thoroughly investigate the effect of supplementary As(V) during biooxidation of arsenopyrite by Acidithiobacillus thiooxidans. It is revealed that arsenic can enhance bacterial reactions during bioleaching, which can strongly influence its mobility. Biofilms occur as compact-flattened microcolonies, being progressively covered by a significant amount of secondary compounds (S _n ^2- , S⁰, pyrite-like). Biooxidation mechanism is modified in the presence of supplementary As(V), as indicated by spectroscopic and microscopic studies. GDS confirms significant variations between abiotic control and biooxidized arsenopyrite in terms of surface reactivity and amount of secondary compounds with and without As(V) (i.e. 6 μm depth). CLSM and protein analyses indicate a rapid modification in biofilm from hydrophilic to hydrophobic character (i.e. 1–12 h), in spite of the decrease in extracellular surface proteins in the presence of supplementary As(V) (i.e. stressed biofilms).     

Effects of Plasmodium gallinaceum on hemolymph physiology of Aedes aegypti during parasite development

Insect disease vectors show diminished fecundity when infected with Plasmodium. This phenomenon has already been demonstrated in laboratory models such as Aedes aegypti, Anopheles gambiae and Anopheles stephensi. This study demonstrates several changes in physiological processes of A. aegypti occurring upon infection with Plasmodium gallinaceum, such as reduced ecdysteroid levels in hemolymph as well as altered expression patterns for genes involved in vitellogenesis, lipid transport and immune response. Furthermore, we could show that P. gallinaceum infected A. aegypti presented a reduction in reproductive fitness, accompanied by an activated innate immune response and increase in lipophorin expression, with the latter possibly representing a nutritional resource for Plasmodium sporozoites.     

Phospholipid-Derived Fatty Acids and Quinones as Markers for Bacterial Biomass and Community Structure in Marine Sediments

Phospholipid-derived fatty acids (PLFA) and respiratory quinones (RQ) are microbial compounds that have been utilized as biomarkers to quantify bacterial biomass and to characterize microbial community structure in sediments, waters, and soils. While PLFAs have been widely used as quantitative bacterial biomarkers in marine sediments, applications of quinone analysis in marine sediments are very limited. In this study, we investigated the relation between both groups of bacterial biomarkers in a broad range of marine sediments from the intertidal zone to the deep sea. We found a good log-log correlation between concentrations of bacterial PLFA and RQ over several orders of magnitude. This relationship is probably due to metabolic variation in quinone concentrations in bacterial cells in different environments, whereas PLFA concentrations are relatively stable under different conditions. We also found a good agreement in the community structure classifications based on the bacterial PLFAs and RQs. These results strengthen the application of both compounds as quantitative bacterial biomarkers. Moreover, the bacterial PLFA- and RQ profiles revealed a comparable dissimilarity pattern of the sampled sediments, but with a higher level of dissimilarity for the RQs. This means that the quinone method has a higher resolution for resolving differences in bacterial community composition. Combining PLFA and quinone analysis as a complementary method is a good strategy to yield higher resolving power in bacterial community structure.     

Resistance of the AF-28 sorghum variety to Contarinia sorghicola

The variety AF-28 of Sorghum bicolor Pers and the hybrid R-1090 were compared in relation to the sorghum midge, Contarinia sorghicola (Coquillet), (Diptera: Cecidomyidae) in two counties of the State of São Paulo. They were compared in seven successive monthly trials beginning in September 1972. Averages of 252 and 137 adult flies emerged per head of the hybrid R-1090 in Campinas and Jaboticabal respectively, while 2.9 and 0.8 emerged from AF-28. The damage was graded with a visual scale from 0 to 4. Average damage grades of 3.5 and 3.3 were attributed to the hybrid R-1090 in Campinas and Jaboticabal respectively, while the variety AF-28 had averages of 0.5 and 0.3, respectively.

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Résumé La variété AF-28 et l'hybride R-1090 de Sorghum bicolor Pers. ont été comparés à différentes époques de l'année et en deux localités différentes de l'Etat de Sâo Paulo, Brésil.On n'a pas constaté d'interaction variété x époque ou variété x lieu.AF-28 a prouvé sa résistance à toutes les époques, aussi bien dans un lieu que dans l'autre; l'hybride par contre s'est montré grandement susceptible.Des moyennes de 252,2 et 136,7 mouches par panicule ont été observées pour l'hybride R-1090 à Campinas et à Jaboticabal contre 2,9 et 0,8 seulement par panicule de AF-28. Le préjudice a été estimé visuellement selon une échelle de 0 à 4. Des préjudices d'une valeur moyenne de 3,5 et 3,3 ont été attribués à l'hybride R-1090 à Campinas et à Jaboticabal respectivement, alors que simultanément la variété AF-28 ne subissait que des préjudices évalués à 0,5 et 0,3 respectivement.Quatre espèces de microhyménoptères parasites de Contarinia sorghicola ont été récoltées au cours de ce travail: Eupelmus popa et trois espèces différentes du genre Tetrastichus.

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Part of a thesis presented to the School of Sciences of Bauru for fulfilment of the requirement for the degree of Doctor of Science. This research was financed by the Project 72/1471 of the agreement UNIÃO-ESTADO-FAPESP and by CNPq Project 12910/73.