Benthic invertebrates that form habitat on deep banks off southern California, with special reference to deep sea coral

There is increasing interest in the potential impacts that fishing activities have on megafaunal benthic invertebrates occurring in continental shelf and slope ecosystems. We examined how the structure, size, and high-density aggregations of invertebrates provided structural relief for fishes in continental shelf and slope ecosystems off southern California. We made 112 dives in a submersible at 32−320 m water depth, surveying a variety of habitats from high-relief rock to flat sand and mud. Using quantitative video transect methods, we made 12,360 observations of 15 structure-form-ing invertebrate taxa and 521,898 individuals. We estimated size and incidence of epizoic animals on 9105 sponges, black corals, and gorgonians. Size variation among structure-form-ing invertebrates was significant and 90% of the individuals were <0.5 m high. Less than 1% of the observations of organisms actually sheltering in or located on invertebrates involved fishes. From the analysis of spatial associations between fishes and large invertebrates, six of 108 fish species were found more often adjacent to invertebrate colonies than the number of fish predicted by the fish-density data from transects. This finding indicates that there may be spatial associations that do not necessarily include physical contact with the sponges and corals. However, the median distances between these six fish species and the invertebrates were not particularly small (1.0−5.5 m). Thus, it is likely that these fishes and invertebrates are present together in the same habitats but that there is not necessarily a functional relationship between these groups of organisms. Regardless of their associations with fishes, these invertebrates provide structure and diversity for continental shelf ecosystems off southern California and certainly deserve the attention of scientists undertaking future conservation efforts

Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis

Sulfur cycling is ubiquitous in sedimentary environments, where it plays a major role in mediating carbon remineralization and impacts both local and global redox budgets. Microbial sulfur cycling is dominated by metabolic activity that either produces (e.g., sulfate reduction, disproportionation) or consumes (sulfide oxidation) hydrogen sulfide (H2S). As such, improved constraints on the production, distribution, and consumption of H2S in the natural environment will increase our understanding of microbial sulfur cycling. These different microbial sulfur metabolisms are additionally associated with particular stable isotopic fractionations. Coupling measurements of the isotopic composition of the sulfide with its distribution can provide additional information about environmental conditions and microbial ecology. Here we investigate the kinetics of sulfide capture on photographic films as a way to document the spatial distribution of sulfide in complex natural environments as well as for in situ capture of H2S for subsequent stable isotopic analysis. Laboratory experiments and timed field deployments demonstrate the ability to infer ambient sulfide abundances from the yield of sulfide on the films. This captured sulfide preserves the isotopic composition of the ambient sulfide, offset to slightly lower δ34S values by ~ 1.2 ± 0.5‰ associated with the diffusion of sulfide into the film and subsequent reaction with silver to form Ag2S precipitates. The resulting data enable the exploration of cm-scale lateral heterogeneity that complement most geochemical profiles using traditional techniques in natural environments. Because these films can easily be deployed over a large spatial area, they are also ideal for real-time assessment of the spatial and temporal dynamics of a site during initial reconnaissance and for integration over long timescales to capture ephemeral processes

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient

• Changes in species richness and distributions of ectomycorrhizal (ECM) fungal communities along altitudinal gradients have been attributed to changes in both host distributions and abiotic variables. However, few studies have considered altitudinal relationships of ECM fungi associated with a single host to identify the role of abiotic drivers. To address this, ECM fungal communities associated with one host were assessed along five altitudinal transects in Scotland. • Roots of Scots pine (Pinus sylvestris) were collected from sites between 300 and 550–600 m altitude, and ECM fungal communities were identified by 454 pyrosequencing of the fungal internal transcribed spacer (ITS) region. Soil moisture, temperature, pH, carbon : nitrogen (C : N) ratio and organic matter content were measured as potential predictors of fungal species richness and community composition. • Altitude did not affect species richness of ECM fungal communities, but strongly influenced fungal community composition. Shifts in community composition along the altitudinal gradient were most clearly related to changes in soil moisture and temperature. • Our results show that a 300 m altitudinal gradient produced distinct shifts in ECM fungal communities associated with a single host, and that this pattern was strongly related to climatic variables. This finding suggests significant climatic niche partitioning among ECM fungal species

Bioencapsulation and Colonization Characteristics of Lactococcus lactis subsp. lactis CF4MRS in Artemia franciscana: a Biological Approach for the Control of Edwardsiellosis in Larviculture

Predominance of beneficial bacteria helps to establish a healthy microbiota in fish gastrointestinal system and thus to reduce emerging pathogen. In this study, the colonization efficacy of Lactococcus lactis subsp. lactis CF4MRS in Artemia franciscana and its potential as a probiotic in suppressing Edwardsiella sp. infection were investigated in vivo. The colonization extent of the bioencapsulated L. lactis was established through visualization of gfp gene-transformed L. lactis in A. franciscana. Here, we demonstrate that when A. franciscana is administrated with L. lactis at 108 CFU mL−1 for 8 h, the highest relative percentage of survival (RPS = 50.0) is observed after inoculation with Edwardsiella sp. The total counts of L. lactis entrapped in Artemia were the highest (ranged from 3.2 to 5.1 × 108 CFU mL−1), when 108–109 CFU mL−1 of L. lactis was used as starting inoculum, with the bioencapsulation performed within 8–24 h. Fluorescent microscopy showed gfp-transformed L. lactis colonized the external trunk surfaces, mid-gut and locomotion antennules of the A. franciscana nauplii. These illustrations elucidate the efficiency of colonization of L. lactis in the gastrointestinal tract and on the body surfaces of Artemia. In conclusion, L. lactis subsp. lactis CF4MRS shows a good efficacy of colonization in Artemia and has the potential for biocontrol/probiotic activity against Edwardsiella sp. infection

Effect of Hydrogen Peroxide on Immersion Challenge of Rainbow Trout Fry with Flavobacterium psychrophilum

An experimental model for immersion challenge of rainbow trout fry (Oncorhynchus mykiss) with Flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome and bacterial cold water disease was established in the present study. Although injection-based infection models are reliable and produce high levels of mortality attempts to establish a reproducible immersion model have been less successful. Various concentrations of hydrogen peroxide (H₂O₂) were evaluated before being used as a pre-treatment stressor prior to immersion exposure to F. psychrophilum. H₂O₂ accelerated the onset of mortality and increased mortality approximately two-fold; from 9.1% to 19.2% and from 14.7% to 30.3% in two separate experiments. Clinical signs observed in the infected fish corresponded to symptoms characteristically seen during natural outbreaks. These findings indicate that pre-treatment with H₂O₂ can increase the level of mortality in rainbow trout fry after exposure to F. psychrophilum

Genomic Description of ‘Candidatus Abyssubacteria,’ a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes

The subsurface biosphere is a massive repository of fixed carbon, harboring approximately 90% of Earth’s microbial biomass. These microbial communities drive transformations central to Earth’s biogeochemical cycles. However, there is still much we do not understand about how complex subterranean microbial communities survive and how they interact with these cycles. Recent metagenomic investigation of deeply circulating terrestrial subsurface fluids revealed the presence of several novel lineages of bacteria. In one particular example, phylogenomic analyses do not converge on any one previously identified taxon; here we describe the first full genomic sequences of a new bacterial lineage within the candidate phylum Hydrogenedentes, ‘Candidatus Abyssubacteria.’ A global survey revealed that members of this proposed lineage are widely distributed in both marine and terrestrial subsurface environments, but their physiological and ecological roles have remained unexplored. Two high quality metagenome assembled genomes (SURF_5: 97%, 4%; SURF_17: 91% and 4% completeness and contamination, respectively) were reconstructed from fluids collected 1.5 kilometers below surface in the former Homestake gold mine—now the Sanford Underground Research Facility (SURF)—in Lead, South Dakota, United States. Metabolic reconstruction suggests versatile metabolic capability, including possible nitrogen reduction, sulfite oxidation, sulfate reduction and homoacetogenesis. This first glimpse into the metabolic capabilities of these cosmopolitan bacteria suggests that they are involved in key geochemical processes, including sulfur, nitrogen, and carbon cycling, and that they are adapted to survival in the dark, often anoxic, subsurface biosphere