Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (−5°C), hypersalinity (salinity, 24%), and reducing (≈−165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H₂S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day⁻¹). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.     

Prokaryotic Abundance and Community Composition in a Freshwater Iron-Rich Microbial Mat at Circumneutral pH

The abundance, diversity and composition of bacterial and archaeal communities in a freshwater iron-rich microbial mat were investigated using culture-dependent and culture-independent methods. The sampling site is a mixing zone where ferrous-iron-rich fluids encounter oxygen-rich environments. Quantitative PCR analysis shows that Bacteria dominated the mat community (>99% of the total cell numbers). Phylotypes related to iron-oxidizers in Gallionellaceae, methano/methylotrophs in Methylophilaceae and Methylococcaceae, sulfide-oxidizers in Sulfuricurvum and an uncultured clone group, called Terrestrial group I or the 1068 group, in the Epsilonproteobacteria were detected in the clone library from the original sample and/or the enrichment cultures. This result suggests that these members may play a role in Fe, S and C cycling in the mixing zone. Although Archaea were minor constituents numerically, phylogenetic analysis indicates that unique and diverse yet-uncultivated Archaea are present in the iron-rich mat. The phylotypes of these yet-uncultivated Archaea belong to environmental clone groups that have been recovered from other mixing zones in terrestrial and marine environments, and some of our phylotypes have significantly low similarity (80% or lower) with the archaeal clones reported previously. Our results provide further insights into the bacterial and archaeal communities in a microaerobic iron-rich freshwater environment in mixing zones.     

Viral production in the Gulf of Trieste (Northern Adriatic Sea): Preliminary results using different methodological approaches

Although the temporal and spatial variability of virioplankton in the northernmost part of the Adriatic Sea has been repeatedly explored suggesting that viruses constitute an extremely dynamic component of the plankton community and hypothesizing their importance in marine food webs and mucilage events, there is still no information about viral replication rates. Hence, the contribution of viruses to bacterial mortality and the cycling of organic matter in this part of the Adriatic basin are still not fully comprehended. Assessment of the role of viral lysis requires a robust means of estimating viral production. Since, up to now, none of the available methods evolved to a state of a standard yet, in this preliminary study 3 different experimental approaches were simultaneously assayed (viral production estimated by radiotracer incorporation method [TdR], dilution technique for the estimate of viral production in already infected bacteria [DIL] and serial dilution method in manipulated phage-host assemblage [SER]). The present study provided the first evidence of viral production rates in this study area, that resulted in comprising between ∼ 3.5-15 × 10⁸ viruses L^− 1 h^− 1 and critically faced up the results obtained by different techniques with the consideration that they suffer from different biases. Based on TdR and DIL viral proliferation estimates, viral lysis was responsible for the loss of 54 to 95% of the bacterial standing stock, while the viral-induced mortality by SER (325% d^− 1) was likely consistently overestimated. These results indicate that viral lysis is a significant factor for prokaryotic mortality suggesting its implication as an important pathway for the cycling of dissolved organic matter in the Gulf of Trieste.     

Quaranfil,Johnston Atoll,and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae

Arboviral infections are an important cause of emerging infections due to the movements of humans, animals, and hematophagous arthropods. Quaranfil virus (QRFV) is an unclassified arbovirus originally isolated from children with mild febrile illness in Quaranfil, Egypt, in 1953. It has subsequently been isolated in multiple geographic areas from ticks and birds. We used high-throughput sequencing to classify QRFV as a novel orthomyxovirus. The genome of this virus is comprised of multiple RNA segments; five were completely sequenced. Proteins with limited amino acid similarity to conserved domains in polymerase (PA, PB1, and PB2) and hemagglutinin (HA) genes from known orthomyxoviruses were predicted to be present in four of the segments. The fifth sequenced segment shared no detectable similarity to any protein and is of uncertain function. The end-terminal sequences of QRFV are conserved between segments and are different from those of the known orthomyxovirus genera. QRFV is known to cross-react serologically with two other unclassified viruses, Johnston Atoll virus (JAV) and Lake Chad virus (LKCV). The complete open reading frames of PB1 and HA were sequenced for JAV, while a fragment of PB1 of LKCV was identified by mass sequencing. QRFV and JAV PB1 and HA shared 80% and 70% amino acid identity to each other, respectively; the LKCV PB1 fragment shared 83% amino acid identity with the corresponding region of QRFV PB1. Based on phylogenetic analyses, virion ultrastructural features, and the unique end-terminal sequences identified, we propose that QRFV, JAV, and LKCV comprise a novel genus of the family Orthomyxoviridae.Arboviral infections are an important and emerging cause of human illness. Recent epidemics of West Nile, chikungunya, dengue, and yellow fever illustrate the importance of understanding the basic virology of arboviruses. Quaranfil virus (QRFV) is a heretofore-unclassified arbovirus isolated in 1953 from ticks (Argas [Persicargus] arboreus) collected near Cairo, Egypt, and subsequently passaged in mice and Vero cells. This tick-derived isolate was determined by serologic methods to be related to a virus previously cultured from the blood of two children with mild febrile illnesses in Quaranfil, Egypt (32). Human serologic studies performed in the 1960s in Egypt revealed that approximately 8% of the local population had neutralizing antibodies to this virus, demonstrating that human infection occurs and raising the question of whether QRFV might represent an unrecognized cause of viral illness in humans (32). The extent to which this virus may cause clinical illness in people is currently unknown; however, multiple strains of QRFV have been isolated from ticks and seabirds in Egypt, South Africa, Afghanistan, Nigeria, Kuwait, Iraq, Yemen, and Iran (1, 12, 20, 29, 30). QRFV is lethal after intracerebral (i.c.) inoculation of newborn mice (32). One study reported that experimental QRFV infection of laboratory mice causes a lethal respiratory disease and meningoencephalitis (4).Johnston Atoll virus (JAV) was originally isolated from ticks (Ornithodoros capensis) collected in 1964 from a Noddy Tern (Anous stolidus) nest, Sand Island, Johnston Atoll in the central Pacific (11). Multiple strains have subsequently been isolated from eastern Australia, New Zealand, and Hawaii (3). No human disease has been associated with JAV, but it is lethal to newborn and weanling mice after i.c. injection and to 1- to 2-day-old chicks after subcutaneous inoculation. (11). Lake Chad virus (LKCV), strain Ib An 38918, was isolated from a masked weaver bird, Ploceus vitellinus, collected at Lake Chad, Nigeria, in 1969. LKCV is lethal to newborn mice after i.c. inoculation, and it was shown to be antigenically related to QRFV (R. E. Shope, personnel communication).To date, conventional approaches to characterize QRFV, JAV, and LKCV have not resulted in a definitive classification of these viruses. QRFV and JAV are enveloped RNA viruses, and electron microscopic and serologic studies tentatively suggested a classification in the arenavirus family based on morphological and morphogenetic features of the viruses (38). In this study, we utilized high-throughput sequencing to identify genomic sequences from QRFV, JAV, and LKCV. Based on analysis of the complete sequences of five of these segments from QRFV and partial sequences from JAV and LKCV, ultrastructural analysis of infected cell cultures, and serologic testing, we propose that these viruses define a novel genus in the family Orthomyxoviridae.     

A Cell Culture Adapted HCV JFH1 Variant That Increases Viral Titers and Permits the Production of High Titer Infectious Chimeric Reporter Viruses

The unique properties of the hepatitis C virus (HCV) JFH1 isolate have made it possible to produce and study HCV in an infectious cell culture system. However, relatively low virus titers restrict some of the uses of this system and preparing infectious chimeric reporter viruses have been difficult. In this study, we report cell culture-adapted mutations in wild-type JFH1 yielding higher titers of infectious particles of both JFH1 and chimeric JFH1 viruses carrying reporter genes. Sequencing analyses determined that ten of the sixteen nonsynonymous mutations were in the NS5A region. Individual viruses harboring specific adaptive mutations were prepared and studied. The mutations in the NS5A region, which included all three domains, were most effective in increasing infectious virus production. Insertion of two reporter genes in JFH1 without the adaptive mutations ablated the production of infectious HCV particles. However, the introduction of specific adaptive mutations in the NS5A region permitted reporter genes, Renilla luciferase (Rluc) and EGFP, to be introduced into JHF1 to produce chimeric HCV-NS5A-EGFP and HCV-NS5A-Rluc reporter viruses at relatively high titers of infectious virus. The quantity of hyperphosphorylated NS5A (p58) was decreased in the adapted JFH1 compared wild type JFH1 and is likely be involved in increased production of infectious virus based on previous studies of p58. The JFH1-derived mutant viruses and chimeric reporter viruses described here provide new tools for studying HCV biology, identifying HCV antivirals, and enable new ways of engineering additional infectious chimeric viruses.     

Native and non-native ctenophores in the Gulf of Trieste, Northern Adriatic Sea

Observations of ctenophore species were made in the Gulf ofTrieste between 2003 and 2006. We examined native ctenophorespecies with special attention to representatives of the ordersLobata and Beroida, and we recorded among them two non-nativectenophores: Mnemiopsis leidyi A. Agassiz 1865 and Beroe ovatasensu Mayer, 1912. The validity of the Mediterranean speciesBeroe ovata is discussed. We determined that among the nativespecies, it is not Beroe ovata but rather Beroe cucumis sensuMayer, 1912 that occurs in the Mediterranean Sea.     

Microbial Dynamics of an Epilithic Mat Community in a High Alpine Stream

Studies were conducted to examine interrelationships between the heterotrophic and phototrophic populations within an epilithic community in the outlet stream of a high alpine lake. Levels of nitrates, phosphates, and total organic compounds in the lake were consistently near the lower limits of detectability. Microscopic examination of the community by phase-contrast light microscopy and scanning electron microscopy revealed diatoms, filamentous algae, and bacteria embedded within a dense gelatinous matrix. Chlorophyll a and primary productivity measurements had peak values in early August, with subsequent declines. Bacterial heterotrophic activity, as measured by V_max, turnover rate, and relative activity, increased significantly as the phototrophic community declined. This trend in heterotrophic activity was not accompanied by an increase in total bacterial numbers as determined by epi-illuminated fluorescence microscopy. These results suggest that the phototrophic community responded to changes in, or interactions among, various chemical and physical factors throughout the study period. The catabolic activity of the sessile bacteria appeared to be positively influenced by changes in the mat environment resulting from the decline of the phototrophic populations.     

Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes

CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B′) as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B′ genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B′, but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as “viritopes” to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.     

Abundance and Community Structure of Picoplankton and Protists in the Microbial Food Web of Barguzin Bay,Lake Baikal

We examined the vertical abundance of bacteria, phytoplankton and protists along a transect of six stations from near-shore (Stn. 1) to off-shore (Stn. 6) in Barguzin Bay of Lake Baikal, in the summer of 2002. Chlorophyll concentrations at Stn. 1 were higher (>10μg l⁻¹) than at the other five stations (<3μg l⁻¹). Planktonic and sessile diatoms dominated at Stn. 1, while pico-phytoplankon was dominant at other stations. Densities of heterotrophic bacteria were high in both the epilimnion and the thermocline at all stations. Nanoflagellates were abundant in the epilimnion, and ciliates in the thermocline, but no horizontal trend could be found for these heterotrophs. At Stn. 1, not only filter feeding (Strombidium and Strobilidium) and raptorial (Balanion) ciliates but also predatory ciliates (Prorodon and Spathidiosus) dominated, while at other stations only the filter feeding and raptorial ciliates were dominant. In off-shore stations (Stns. 5 and 6), significant correlations were detected between concentrations of chlorophyll a and density of filter feeding or raptorial ciliates, suggesting tight food linkages between phytoplankton and these ciliates. The concentration of dissolved organic carbon (DOC) was significantly correlated with chlorophyll a concentration, although there was no significant correlation between DOC concentration and bacterial density. We suggest that there is a shift of the dominant food linkage from a herbivorous food chain in near-shore areas to a microbial food web in off-shore areas in Barguzin Bay of Lake Baikal.     

Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.     

Genetic Analyses of HIV-1 env Sequences Demonstrate Limited Compartmentalization in Breast Milk and Suggest Viral Replication within the Breast That Increases with Mastitis

The concentration of human immunodeficiency virus type 1 (HIV-1) is generally lower in breast milk than in blood. Mastitis, or inflammation of the breast, is associated with increased levels of milk HIV-1 and risk of mother-to-child transmission through breastfeeding. We hypothesized that mastitis facilitates the passage of HIV-1 from blood into milk or stimulates virus production within the breast. HIV-1 env sequences were generated from single amplicons obtained from breast milk and blood samples in a cross-sectional study. Viral compartmentalization was evaluated using several statistical methods, including the Slatkin and Maddison (SM) test. Mastitis was defined as an elevated milk sodium (Na⁺) concentration. The association between milk Na⁺ and the pairwise genetic distance between milk and blood viral sequences was modeled using linear regression. HIV-1 was compartmentalized within milk by SM testing in 6/17 (35%) specimens obtained from 9 women, but all phylogenetic clades included viral sequences from milk and blood samples. Monotypic sequences were more prevalent in milk samples than in blood samples (22% versus 13%; P = 0.012), which accounted for half of the compartmentalization observed. Mastitis was not associated with compartmentalization by SM testing (P = 0.621), but Na⁺ was correlated with greater genetic distance between milk and blood HIV-1 populations (P = 0.041). In conclusion, local production of HIV-1 within the breast is suggested by compartmentalization of virus and a higher prevalence of monotypic viruses in milk specimens. However, phylogenetic trees demonstrate extensive mixing of viruses between milk and blood specimens. HIV-1 replication in breast milk appears to increase with inflammation, contributing to higher milk viral loads during mastitis.Breastfeeding accounts for 30 to 50% of mother-to-child-transmission (MTCT) of human immunodeficiency virus type 1 (HIV-1) (38). MTCT through breastfeeding occurs primarily in sub-Saharan Africa, where the use of artificial infant formula is often not feasible because of cost and the associated infant mortality from infections due to the use of unsafe water and the lack of the protective effects of breast milk (19, 38, 51). Numerous strategies to reduce postnatal HIV-1 infection of infants while preserving the advantages of breastfeeding have been evaluated, including maternal use of combination antiretroviral therapy or infant antiretroviral prophylaxis during the period of breastfeeding (5, 25, 26, 30, 40). Understanding the biologic events that increase the concentration of HIV-1 in breast milk is critical to the development and evaluation of interventions to reduce postnatal MTCT.The risk of MTCT is strongly associated with the concentration of HIV-1 in breast milk (28, 46, 47). Although breast milk HIV-1 RNA concentrations correlate with those in plasma, levels in milk are typically 2 log₁₀ lower (15, 24, 43). This suggests that HIV-1 in blood and milk may not mix freely, likely because of the closure of tight junctions between mammary alveolar cells that occurs once milk production is established and before weaning (16). Thus, HIV-1 may evolve in the breast without substantial mixing with blood, i.e., evolving viral variants would become compartmentalized—a phenomenon that has been observed in the central nervous system (50) and in some studies of the genital tract (10, 44, 57). Compartmentalization of HIV-1 variants has been detected in the breast milk of a small number of women (3, 4), but other data suggest that compartmentalization in breast milk may be uncommon (22).Breast inflammation (mastitis) occurs frequently during lactation, most commonly without symptoms. Mastitis is associated with elevations in HIV-1 RNA levels in milk (15, 31, 47, 55), an increase in the number of inflammatory cells in milk, and opening of tight junctions in the mammary epithelium that allows passage of subcellular blood components, of which sodium (Na⁺) serves as a marker (15, 16, 36, 47, 55). Greater permeability of mammary epithelia may allow the passage of free virus from the blood into breast milk, which would result in the mixing of HIV-1 subpopulations from blood and milk. Alternatively, inflammation in the breast may induce replication of virus by HIV-1-infected cells within the breast, which would result in divergence between milk and blood HIV-1 subpopulations. Here we describe detailed genetic analyses of HIV-1 subpopulations in the blood and breast milk to determine whether mastitis affects the structure of these populations and to gain understanding of the processes that may lead to increased concentrations of HIV-1 in milk.     

Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.     

The Wallpaper Effect: The Contact Hypothesis Fails for Minority Group Members Who Live in Areas with a High Proportion of Majority Group Members

We aim to provide one explanation for why the link between contact and prejudice is consistently less strong for minority group members than it is for majority group members. Specifically, we propose a “wallpaper effect” such that contact works to increase minority group members'' positivity towards majority groups when they live in areas densely populated with other minority group members. Conversely, we suggest that when minority group members live in neighborhoods patterned with majority group faces (as is so often the case), contact will be less transformative. We test this assumption using a large sample of both New Zealander minority (Māori; N = 925) and majority (European; N = 3805) group members. In line with predictions, Māori who lived in minority dense neighborhoods showed the traditional association between contact and increased warmth towards New Zealander Europeans. This relationship, however, was weak or non-existent when they lived in primarily European neighborhoods. Contact effects in majority group members were unaffected by neighborhood composition. The interaction held when controlling for, and was not explained by: gender, income, experiences of harm, cognitions of race-based rejection, or realistic threat. We provide the first evidence to suggest that when it comes to minority group members'' intergroup attitudes, contact with majority group members may be a relatively ineffective predictor unless the “wallpaper” of their lives is minority-dense.     

Biodiversity of settled material in a sediment trap in the Gulf of Trieste (northern Adriatic Sea)

Phytoplankton succession and sinking rates were studied from January to December 2003 at a coastal station in the Gulf of Trieste (northern Adriatic Sea), 200 m offshore, in a relatively undisturbed area. A conical sediment trap, moored at 15 m depth (water depth 17 m), was used. The hypothesis if the presence of benthic and epiphytic diatoms can lead to an overestimation of the vertical fluxes was tested. To evaluate primary and secondary sedimentation contributions, planktonic, benthic and epiphytic diatoms were distinguished. Benthic species abundance varied throughout the year and it was related to resuspension that strongly influenced sinking rates. All over the year, diatoms were the prevailing class in the trap material accounting for 75.32% of the settled cells, while flagellates represented 24.11%. Dinophyceae and resting cells constituted minor components, accounting for 0.43% and 0.14%, respectively. The gross sedimentation rates ranged from 0.006 × 10⁸ cell m⁻² d⁻¹ in the second week of May to 6.30 × 10⁸ cell m⁻² d⁻¹ in the third week of January with a mean annual value of 1.09 ± 1.43 × 10⁸ cell m⁻² d⁻¹. To the primary sedimentation rate Pseudo-nitzschia seriata of the group “Nitzschia seriata complex” contributed for 49.77% followed by Chaetoceros spp. (23.88%). The major contributor to the secondary sedimentation rate was the diatom Paralia sulcata, accounting for 24.76%. Epiphytic diatoms contributed for 11.19% and 12.27% on annual average gross abundance and biomass, respectively, reaching even 72.04% of gross abundance and 56.06% of gross biomass in the second week of August. The correlation between temperature and the logarithm of the epiphytic biomass was statistically significant, with r = 0.66 and P < 0.001. Both in the cluster analysis and in the PCA four main groups were formed, where benthic and epiphytic species were separately gathered. Planktonic, benthic and epiphytic forms accounted for 50.78%, 36.95% and 12.27%, respectively, calculated on the annual average biomass. Therefore, vertical fluxes can be overestimated of 50% or more if benthic and epiphytic species are not rejected.     

Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition

Although previous studies have described opposing states in upwelling regions, i.e., the rise of cold nutrient-rich waters and prevalence of surface warm nutrient-poor waters, few have addressed the transition from one state to the other. This study aimed to describe the microbial and viral structure during this transition and was able to obtain the taxonomic and metabolic compositions as well as physical-chemical data. This integrated approach allowed for a better understanding of the dynamics of the downwelling upwelling transition, suggesting that a wealth of metabolic processes and ecological interactions are occurring in the minute fractions of the plankton (femto, pico, nano). These processes and interactions included evidence of microbial predominance during downwelling (with nitrogen recycling and aerobic anoxygenic photosynthesis), different viral predation pressures over primary production in different states (cyanobacteria vs eukaryotes), and a predominance of diatoms and selected bacterial and archaeal groups during upwelling (with the occurrence of a wealth of nitrogen metabolism involving ammonia). Thus, the results provided insights into which microbes, viruses and microbial-mediated processes are probably important in the functioning of upwelling systems.     

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.