A sea-bottom sampler that collects both water and sediment simultaneously

A simple sampler, assembled mainly from commercially available eq uipment, is described. It simultaneously collects water samples at 1, 2, 3, 4, 5, and 6 m above the sea floor and takes a short core at the same location

Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of 15N2 incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages

Metabolic modeling of a mutualistic microbial community

The rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. To enhance our understanding of these relationships, we took advantage of the fully sequenced genomes of Desulfovibrio vulgaris and Methanococcus maripaludis to produce and analyze the first multispecies stoichiometric metabolic model. Model results were compared to data on growth of the co-culture on lactate in the absence of sulfate. The model accurately predicted several ecologically relevant characteristics, including the flux of metabolites and the ratio of D. vulgaris to M. maripaludis cells during growth. In addition, the model and our data suggested that it was possible to eliminate formate as an interspecies electron shuttle, but hydrogen transfer was essential for syntrophic growth. Our work demonstrated that reconstructed metabolic networks and stoichiometric models can serve not only to predict metabolic fluxes and growth phenotypes of single organisms, but also to capture growth parameters and community composition of simple bacterial communities

Correction to: Size matters: biochemical mineralization and microbial incorporation of dicarboxylic acids in soil

The transformation and turnover time of medium- to long-chain dicarboxylic acids (DCA) in soil is regulated by microbial uptake and mineralization. However, the chain length of n-alkyl lipids may have a remarkable influence on its microbial utilization and mineralization and therefore on the formation of stable soil organic carbon from e.g. leave- needle- and root-derived organic matter during decomposition. To investigate their size dependent mineralization and microbial incorporation, four DCA of different chain lengths (12–30 carbon atoms), that were 13C labeled at each of their terminal carboxylic groups, were applied to the Ah horizon of a Fluvic Gleysol. Incorporation of 13C into CO2 and in distinct microbial groups classified by phospholipid fatty acid (PLFA) analysis was investigated. Mineralization of DCA and incorporation into PLFA decreased with increasing chain length, and the mineralization rate was highest during the first days of incubation. Half-life time of DCA carbon in soil increased from 7.6 days for C12 DCA to 86.6 days for C18 DCA and decreased again to 46.2 days for C22 DCA, whereas C30 DCA had the longest half-life time. Rapid and efficient uptake of C12 DCA as an intact molecule was observable. Gram-negative bacteria incorporated higher amounts of DCA-derived 13C compared to other microbial groups, especially compared to actinomycetes and fungi during the first phase of incubation. However, the incorporation of C12 DCA derived 13C into the PLFA of actinomycetes, and fungi increased steadily during the entire incubation time, suggesting that those groups take up the 13C label from necromass of bacteria that used the C12 DCA for formation of their lipids before

Size matters: biochemical mineralization and microbial incorporation of dicarboxylic acids in soil

The transformation and turnover time of medium- to long-chain dicarboxylic acids (DCA) in soil is regulated by microbial uptake and mineralization. However, the chain length of n-alkyl lipids may have a remarkable influence on its microbial utilization and mineralization and therefore on the formation of stable soil organic carbon from e.g. leave- needle- and root-derived organic matter during decomposition. To investigate their size dependent mineralization and microbial incorporation, four DCA of different chain lengths (12–30 carbon atoms), that were 13C labeled at each of their terminal carboxylic groups, were applied to the Ah horizon of a Fluvic Gleysol. Incorporation of 13C into CO2 and in distinct microbial groups classified by phospholipid fatty acid (PLFA) analysis was investigated. Mineralization of DCA and incorporation into PLFA decreased with increasing chain length, and the mineralization rate was highest during the first days of incubation. Half-life time of DCA carbon in soil increased from 7.6 days for C12 DCA to 86.6 days for C18 DCA and decreased again to 46.2 days for C22 DCA, whereas C30 DCA had the longest half-life time. Rapid and efficient uptake of C12 DCA as an intact molecule was observable. Gram-negative bacteria incorporated higher amounts of DCA-derived 13C compared to other microbial groups, especially compared to actinomycetes and fungi during the first phase of incubation. However, the incorporation of C12 DCA derived 13C into the PLFA of actinomycetes, and fungi increased steadily during the entire incubation time, suggesting that those groups take up the 13C label from necromass of bacteria that used the C12 DCA for formation of their lipids before

Evaluation of a temporary vaccination recommendation in response to an outbreak of invasive meningococcal serogroup C disease in men who have sex with men in Berlin, 2013-2014

Meningococcal serogroup C (MenC) vaccination of men who have sex with men (MSM) was temporarily recommended to control an outbreak of invasive MenC disease among MSM in Berlin in 2012–2013. Vaccination was offered to HIV- infected MSM free of charge; others had to request reimbursement or pay out of pocket. We aimed to assess (i) awareness and acceptance of this recommendation through an online survey of MSM, (ii) implementation through a survey of primary care physicians and analysis of vaccine prescriptions, and (iii) impact through analysis of notified cases. Among online survey respondents, 60% were aware of the recommendation. Of these, 39% had obtained vaccination (70% of HIV-infected, 13% of HIV-negative/non-tested MSM). Awareness of recommendation and vaccination were positively associated with HIV infection, primary care physicians’ awareness of respondents’ sexual orientation, and exposure to multiple information sources. Most (26/30) physicians informed clients about the recommendation. Physicians considered concerns regarding reimbursement, vaccine safety and lack of perceived disease risk as primary barriers. After the recommendation, no further outbreak-related cases occurred. To reach and motivate target groups, communication of a new outbreak-related vaccination recommendation should address potential concerns through as many information channels as possible and direct reimbursement of costs should be enabled

Neutrophils promote venular thrombosis by shaping the rheological environment for platelet aggregation

In advanced inflammatory disease, microvascular thrombosis leads to the interruption of blood supply and provokes ischemic tissue injury. Recently, intravascularly adherent leukocytes have been reported to shape the blood flow in their immediate vascular environment. Whether these rheological effects are relevant for microvascular thrombogenesis remains elusive. Employing multi-channel in vivo microscopy, analyses in microfluidic devices, and computational modeling, we identified a previously unanticipated role of leukocytes for microvascular clot formation in inflamed tissue. For this purpose, neutrophils adhere at distinct sites in the microvasculature where these immune cells effectively promote thrombosis by shaping the rheological environment for platelet aggregation. In contrast to larger (lower-shear) vessels, this process in high-shear microvessels does not require fibrin generation or extracellular trap formation, but involves GPIb alpha-vWF and CD40-CD40L-dependent platelet interactions. Conversely, interference with these cellular interactions substantially compromises microvascular clotting. Thus, leukocytes shape the rheological environment in the inflamed venular microvasculature for platelet aggregation thereby effectively promoting the formation of blood clots. Targeting this specific crosstalk between the immune system and the hemostatic system might be instrumental for the prevention and treatment of microvascular thromboembolic pathologies, which are inaccessible to invasive revascularization strategies

Population Dynamics Constrain the Cooperative Evolution of Cross-Feeding

Cross-feeding is the exchange of nutrients among species of microbes. It has two potential evolutionary origins, one as an exchange of metabolic wastes or byproducts among species, the other as a form of cooperation known as reciprocal altruism. This paper explores the conditions favoring the origin of cooperative cross-feeding between two species. There is an extensive literature on the evolution of cooperation, and some of the requirements for the evolution of cooperative cross-feeding follow from this prior work–specifically the requirement that interactions be limited to small groups of individuals, such as colonies in a spatially structured environment. Evolution of cooperative cross-feeding by a species also requires that cross-feeding from the partner species already exists, so that the cooperating mutant will automatically be reciprocated for its actions. Beyond these considerations, some unintuitive dynamical constraints apply. In particular, the benefit of cooperative cross-feeding applies only in the range of intermediate cell densities. At low density, resource concentrations are too low to offset the cost of cooperation. At high density, resources shared by both species become limiting, and the two species become competitors. These considerations suggest that the evolution of cooperative cross-feeding in nature may be more challenging than for other types of cooperation. However, the principles identified here may enable the experimental evolution of cross-feeding, as born out by a recent study