The relative effects of upwelling and river flow on the phytoplankton diversity patterns in the ria of A Coruña (NW Spain)

Phytoplankton species assemblages in estuaries are connected to those in rivers and marine environments by local hydrodynamics leading to a continuous flow of taxa. This study revealed differential effects of upwelling and river flow on phytoplankton communities observed in 2011 along a salinity gradient from a river reservoir connected to the sea through a ria-marine bay system in A Coruña (NW Spain, 43° 16-21’ N, 8° 16-22’ W). With 130 phytoplankton taxa identified, the assemblages were dominated in general by diatoms, particularly abundant in the bay and in the estuary, but also by chlorophycea and cyanobacteria in the reservoir. Considering the entire seasonal cycle, the local assemblages were mainly characterized by changes in cryptophytes and diatoms, small dinoflagellates and some freshwater chlorophycea. Salinity, nitrate, and organic matter variables, were the main environmental factors related to the changes in the phytoplankton communities through the system, while phosphate and nitrite were also important for local communities in the estuary and the bay, respectively. The corresponding local phytoplankton assemblages showed moderate levels of connectivity. The estuarine community shared a variable number of taxa with the adjacent zones, depending on the relative strength of upwelling (major influence from the bay) and river flow (major influence of the reservoir) but had on average 35% of unique taxa. Consequently, local and zonal diversity patterns varied seasonally and were not simply related to the salinity gradient driven by the river flow.ANILE (CTM2009-08396 and CTM2010-08804-E), FIOME (CTM2011-28792-C02-01-MAR), and MEFIO (CTM2011-28792-C02-02-MAR) of the Plan Nacional de I+D+i (Spain), and RADIALES of the Instituto Español de Oceanografía (IEO, Spain).Versión del editor2,01

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota

Our understanding of mammalian evolution has become microbiome-aware. While emerging research links mammalian biodiversity and the gut microbiome, we lack insight into which microbes potentially impact mammalian evolution. Microbes common to diverse mammalian species may be strong candidates, as their absence in the gut may affect how the microbiome functionally contributes to mammalian physiology to adversely affect fitness. Identifying such conserved gut microbes is thus important to ultimately assessing the microbiome’s potential role in mammalian evolution. To advance their discovery, we developed an approach that identifies ancestrally related groups of microbes that distribute across mammals in a way that indicates their collective conservation. These conserved clades are presumed to have evolved a trait in their ancestor that matters to their distribution across mammals and which has been retained among clade members. We found not only that such clades do exist among mammals but also that they appear to be subject to natural selection and characterize human evolution.Our knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals. To advance the discovery of conserved mammalian gut microbes, we developed a novel ecophylogenetic approach to taxonomy that groups microbes into taxonomic units based on their shared ancestry and their common distribution across mammals. Applying this approach to previously generated gut microbiome data uncovered monophyletic clades of gut bacteria that are conserved across mammals. It also resolved microbial clades exclusive to and conserved among particular mammalian lineages. Conserved clades often manifest phylogenetic patterns, such as cophylogeny with their host, that indicate that they are subject to selective processes, such as host filtering. Moreover, this analysis identified variation in the rate at which mammals acquire or lose conserved microbial clades and resolved a human-accelerated loss of conserved clades. Collectively, the data from this study reveal mammalian gut microbiota that possess traits linked to mammalian phylogeny, point to the existence of a core set of microbes that comprise the mammalian gut microbiome, and clarify potential evolutionary or ecologic mechanisms driving the gut microbiome’s diversification throughout mammalian evolution

Age and micronutrient effects on the microbiome in a mouse model of zinc depletion and supplementation.

Older adult populations are at risk for zinc deficiency, which may predispose them to immune dysfunction and age-related chronic inflammation that drives myriad diseases and disorders. Recent work also implicates the gut microbiome in the onset and severity of age-related inflammation, indicating that dietary zinc status and the gut microbiome may interact to impact age-related host immunity. We hypothesize that age-related alterations in the gut microbiome contribute to the demonstrated zinc deficits in host zinc levels and increased inflammation. We tested this hypothesis with a multifactor two-part study design in a C57BL/6 mouse model. The two studies included young (2 month old) and aged (24 month old) mice fed either (1) a zinc adequate or zinc supplemented diet, or (2) a zinc adequate or marginal zinc deficient diet, respectively. Overall microbiome composition did not significantly change with zinc status; beta diversity was driven almost exclusively by age effects. Microbiome differences due to age are evident at all taxonomic levels, with more than half of all taxonomic units significantly different. Furthermore, we found 150 out of 186 genera were significantly different between the two age groups, with Bacteriodes and Parabacteroides being the primary taxa of young and old mice, respectively. These data suggest that modulating individual micronutrient concentrations does not lead to comprehensive microbiome shifts, but rather affects specific components of the gut microbiome. However, a phylogenetic agglomeration technique (ClaaTU) revealed phylogenetic clades that respond to modulation of dietary zinc status and inflammation state in an age-dependent manner. Collectively, these results suggest that a complex interplay exists between host age, gut microbiome composition, and dietary zinc status

Chronic HIV infection enhances the responsiveness of antigen presenting cells to commensal Lactobacillus.

Chronic immune activation despite long-term therapy poses an obstacle to immune recovery in HIV infection. The role of antigen presenting cells (APCs) in chronic immune activation during HIV infection remains to be fully determined. APCs, the frontline of immune defense against pathogens, are capable of distinguishing between pathogens and non-pathogenic, commensal bacteria. We hypothesized that HIV infection induces dysfunction in APC immune recognition and response to some commensal bacteria and that this may promote chronic immune activation. Therefore we examined APC inflammatory cytokine responses to commensal lactobacilli. We found that APCs from HIV-infected patients produced an enhanced inflammatory response to Lactobacillus plantarum WCFS1 as compared to APCs from healthy, HIV-negative controls. Increased APC expression of TLR2 and CD36, signaling through p38-MAPK, and decreased expression of MAP kinase phosphatase-1 (MKP-1) in HIV infection was associated with this heightened immune response. Our findings suggest that chronic HIV infection enhances the responsiveness of APCs to commensal lactobacilli, a mechanism that may partly contribute to chronic immune activation