Latitude and chlorophyll a density drive the distribution of carbohydrate-active enzymes in the planktonic microbial fraction of the epipelagic zone

Microbes drive the majority of the global carbon cycle. The effect of environmental conditions on selecting microbial functional diversity is well established, and recent studies have revealed the effects of geographic distances on selecting the functional components of marine microbial communities. Our study is the first attempt at establishing the effects of environmental factors on driving the marine carbohydrate-active enzyme (CAZyme) distribution. We characterized the diversity of CAZyme genes and investigated the correlations between their distributions and biogeographic parameters (latitude, longitude, distance from the equator, site depth, water depth, chlorophyll density, salinity and temperature). Therefore, we accessed a subset of surface water samples (38 metagenomes) from the Global Ocean Sampling project. Only chlorophyll and latitude altered the distribution patterns of CAZymes, revealing the existence of two latitudinal gradients (positive and negative) of marine CAZyme abundance. Considering the importance of carbohydrates in microbial life, characterization of the spatial patterns of the genetic repertoire involved in carbohydrate metabolism represents an important step in improving our understanding of the metabolic strategies associated with the microbial marine carbon cycle and their effects on the productivity of marine ecosystems.

Five financial incentives to revive the Gulf of Mexico dead zone and Mississippi basin soils

A central challenge in the Mississippi River Basin is how to continue to support profitable agricultural production, provide water supply, flood control, transportation, and other benefits, while reducing the current burden of environmental degradation. Several practices have been shown to reduce nutrient runoff and water pollution, and improve soil fertility, while often yielding profits for farmers. Yet many of these beneficial practices remain underutilized. Participants at an expert workshop identified five candidate financial mechanisms that could increase adoption of these beneficial farming practices in four focal Midwest states in the next five years: crop insurance premium subsidies, transformation of the private service provider business model, expansion and targeting of 2019 U.S. Farm Bill funding, development of new state funds, and direction of post-disaster federal funds towards habitat restoration, particularly in floodplains. This study provides rough approximations of the change in nutrient runoff and greenhouse gas (GHG) emissions, the annualized costs, and the nutrient and GHG reductions per dollar likely to result from deployment of each financial mechanism. Based upon these approximations, the adoption of these programs could reduce annual nitrate flows at the outlet of the Ohio and Upper Mississippi River Basins by 25%, surpassing the intermediate 2025 target (20% reduction) and achieving more than half of the long-term target (45% reduction) set by the Mississippi River/Gulf of Mexico Hypoxia Task Force. These approximations also illustrate that these five mechanisms could provide the same GHG reductions (∼43 Tg CO₂e yr^-1) as taking 12 coal-fired energy plants offline. The total cost of these five financial mechanisms is estimated at ∼$2.6 billion, or 64 g of nitrates and ∼17 kg of CO₂e per dollar spent. These proposed solutions all face political, financial, cultural or institutional challenges, but with industry support, creative political action, and continued communication of both private and public benefits, they can create meaningful nutrient reductions and rebuild soils by 2022.

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption

Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2), on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 'future conditions', with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production.

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

Background

Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools.

Methods

We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification.

Results

We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1.49), low species richness (4.91 ± 0.66), and higher genome completeness (40.92 ± 1.75) across all projects. MetaBat extracted 115 bins from the 4 projects of which 66 bins were identified as reconstructed metagenome-assembled genomes with sequences belonging to a specific genus. We identified 13 novel genomes, some of which were 100% complete, but show low similarity to genomes within databases.

Conclusions

In conclusion, we present a set of biologically relevant parameters for evaluation to select for optimal assembly and binning tools. For the tools we tested, SPAdes assembler and MetaBat binning tools reconstructed quality metagenome-assembled genomes for the four projects. We also conclude that metagenomes from microbial communities that have high coverage of phylogenetically distinct, and low taxonomic diversity results in highest quality metagenome-assembled genomes.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4294-1) contains supplementary material, which is available to authorized users.

Exposure of farm laborers and dairy cattle to formaldehyde from footbath use at a dairy farm in New York State

Formalin footbaths are commonly used in the dairy industry to prevent cattle hoof diseases. Although formalin is a well-documented disinfectant, it is also a carcinogen and irritant. The aim of this study was to estimate the exposure of farm workers and dairy cattle to formaldehyde from footbaths located in a milking facility and a heifer facility at a dairy farm in western New York, USA. The dairy farm included approximately 3900 dairy cattle including young stock; of these, 1670 cows were milked three times per day in a 60-stall carousel milking parlor, and approximately 800 heifers were located at the heifer facility where footbaths with formalin were in use. The formaldehyde concentration of the air was measured using a Formaldemeter™ htV approximately 50cm above the 3% formalin footbaths in the milking (one footbath location) and heifer (three footbath locations) facilities on three consecutive days. The measured formaldehyde concentrations varied between 0.00 and 2.28ppm, falling within the safety guidelines established by the Occupation Safety and Health Administration (OSHA) of the United States. Significant differences were found in the formaldehyde concentrations at the different footbath locations in the heifer facility, potentially due to the varying levels of ventilation at each location. Changes in the ambient temperature during the 3-day sampling period did not significantly affect the concentrations. We believe that the substantial ventilation at both the heifer and milking facilities ensured that the formaldehyde concentrations did not exceed OSHA guidelines, thus permitting the safe use of formalin footbaths in this farm.

Keratoprosthesis in end-stage dry eye

Five cases with end-stage dry eye (four with pemphigoid, one with Stevens-Johnson syndrome) have been operated with a keratoprosthesis and have been followed for followed for 6 to 22 months. Two patients have been failures, three still have good vision.