A metagenomic analysis of the virome of honey bees (
) from an apiary with high rates of unexplained colony losses identified a novel RNA virus. The virus, which was named
solinvivirus 1 (AmSV1), ...contains a 10.6 kb positive-strand genomic RNA with a single ORF coding for a polyprotein with the protease, helicase, and RNA-dependent RNA polymerase domains, as well as a single jelly-roll structural protein domain, showing highest similarity with viruses in the family
. The injection of honey bee pupae with AmSV1 preparation showed an increase in virus titer and the accumulation of the negative-strand of AmSV1 RNA 3 days after injection, indicating the replication of AmSV1. In the infected worker bees, AmSV1 was present in heads, thoraxes, and abdomens, indicating that this virus causes systemic infection. An analysis of the geographic and historic distribution of AmSV1, using over 900 apiary samples collected across the United States, showed AmSV1 presence since at least 2010. In the year 2021, AmSV1 was detected in 10.45% of apiaries (95%CI: 8.41-12.79%), mostly sampled in June and July in Northwestern and Northeastern United States. The diagnostic methods and information on the AmSV1 distribution will be used to investigate the connection of AmSV1 to honey bee colony losses.
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•First to spatially analyze long-term honey bee colony loss data across entire U.S.•Results show spatial approach is essential for investigating honey bee colony loss.•Nov. mean max. ...temperature and Feb. mean precipitation were predictors of loss.•Weather conditions during winter better predict winter loss at the national scale.
Western honey bees (Apis mellifera) have experienced elevated rates of colony loss over the past decade. Past studies have attempted to determine what factors are behind these losses; however, few have considered the effects of environmental variables; key drivers in ecological systems. Existing investigations were conducted at local spatial scales, over small geographic areas, and failed to measure how environmental variables may influence colony loss rates differently across space. Here, we sought to determine the ability of environmental variables to explain honey bee colony winter loss rates across the contiguous U.S. over a nine-year study period, while elucidating how spatial methods produce results which differ from non-spatial approaches. To conduct this study, loss data from stationary beekeepers were obtained from the Bee Informed Partnership’s national Colony Loss and Management Survey for winters spanning from 2011 to 2019 and were aggregated by zip code. Environmental data (i.e., temperature, precipitation, relative humidity, wind speed, elevation) were obtained from PRISM, the Global Wind Atlas, and the U.S. Geological Survey, and averaged by month across the study period. Environmental variables and loss were regressed using linear and geographically weighted regressions. Results demonstrated that effects of environmental variables on colony loss varied across space, indicating that spatial models should be used when studying honey bee colony losses. Additionally, we found that increased winter colony loss rates were linked to lower November mean maximum temperatures and less February mean precipitation, thus, these two variables may be good predictors of observed winter loss rates. Finally, results also revealed that weather conditions during winter months were better predictors of winter colony loss than conditions during other months of the year. Overall, our results illustrate how environmental factors strongly impact managed honey bees and highlight the importance of regionally specific management practices to help prevent losses in the future.
Managed honey bee colony losses are of concern in the USA and globally. This survey, which documents the rate of colony loss in the USA during the 2015-2016 season, is the tenth report of winter ...losses, and the fifth of summer and annual losses. Our results summarize the responses of 5725 valid survey respondents, who collectively managed 427,652 colonies on 1 October 2015, an estimated 16.1% of all managed colonies in the USA. Responding beekeepers reported a total annual colony loss of 40.5% 95% CI 39.8-41.1% between 1 April 2015 and 1 April 2016. Total winter colony loss was 26.9% 95% CI 26.4-27.4% while total summer colony loss was 23.6% 95% CI 23.0-24.1%, making this the third consecutive year when summer losses have approximated to winter losses. Across all operation types, 32.3% of responding beekeepers reported no winter losses. Whilst the loss rate in the winter of 2015-2016 was amongst the lowest winter losses recorded over the ten years this survey has been conducted, 59.0% (n = 3378) of responding beekeepers had higher losses than they deemed acceptable.
Declines of pollinators and high mortality rates of honey bee colonies are a major concern, both in the USA and globally. Long-term data on summer, winter, and annual colony losses improve our ...understanding of forces shaping the viability of the pollination industry. Since the mass die-offs of colonies in the USA during the winter of 2006-2007, generally termed "Colony Collapse Disorder" (CCD), annual colony loss surveys have been conducted. These surveys gage colony losses among beekeepers of all operation sizes, recruited to participate via regional beekeeping organizations, phone calls, and postal mail. In the last three years, these surveys include summer and annual losses in addition to winter losses. Winter losses in this most recent survey include 5,937 valid participants (5,690 backyard, 169 sideline, and 78 commercial beekeepers), collectively managing 414,267 colonies on 1 October 2014 and constituting 15.1% of the estimated 2.74 million managed colonies in the USA. Annual losses are typically higher than either winter or summer losses, as they calculate losses over the entire year. Total reported losses were 25.3% 95% CI 24.7-25.9% over the summer, 22.3% 95% CI 21.9-22.8% over the winter, and 40.6% 95% CI 40.0-41.2% for the entire 2014-2015 beekeeping year. Average losses were 14.7% 95% CI 14.0-15.3% over the summer, 43.7% 95% CI 42.8-44.6% over the winter, and 49.0% 95% CI 48.1-50.0% over the entire year. While total winter losses were lower in 2014-2015 than in previous years, summer losses remained high, resulting in total annual colony losses of more than 40% during the survey period. This was the first year that total losses were higher in the summer than in the winter, explained in large part by commercial beekeepers reporting losses of 26.2% of their managed colonies during summer, compared to 20.5% during winter. Self-identified causes of overwintering mortality differed by operation size, with smaller backyard beekeepers generally indicating colony management issues (e.g., starvation, weak colony in the fall), in contrast to commercial beekeepers who typically emphasize parasites or factors outside their control (e.g., varroa, nosema, queen failure). More than two-thirds of all beekeepers (67.3%) had higher colony losses than they deemed acceptable.
A metagenomic analysis of the virome of honey bees (Apis mellifera) from an apiary with high rates of unexplained colony losses identified a novel RNA virus. The virus, which was named Apis mellifera ...solinvivirus 1 (AmSV1), contains a 10.6 kb positive-strand genomic RNA with a single ORF coding for a polyprotein with the protease, helicase, and RNA-dependent RNA polymerase domains, as well as a single jelly-roll structural protein domain, showing highest similarity with viruses in the family Solinviviridae. The injection of honey bee pupae with AmSV1 preparation showed an increase in virus titer and the accumulation of the negative-strand of AmSV1 RNA 3 days after injection, indicating the replication of AmSV1. In the infected worker bees, AmSV1 was present in heads, thoraxes, and abdomens, indicating that this virus causes systemic infection. An analysis of the geographic and historic distribution of AmSV1, using over 900 apiary samples collected across the United States, showed AmSV1 presence since at least 2010. In the year 2021, AmSV1 was detected in 10.45% of apiaries (95%CI: 8.41–12.79%), mostly sampled in June and July in Northwestern and Northeastern United States. The diagnostic methods and information on the AmSV1 distribution will be used to investigate the connection of AmSV1 to honey bee colony losses.
Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is ...detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of
strains within the
microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a
strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of
isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a
isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative
uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics.
Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as "souring") is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.
The widespread presence of autoantibodies in acute infection with SARS-CoV-2 is increasingly recognized, but the prevalence of autoantibodies in non-SARS-CoV-2 infections and critical illness has not ...yet been reported. We profiled IgG autoantibodies in 267 patients from 5 independent cohorts with non-SARS-CoV-2 viral, bacterial, and noninfectious critical illness. Serum samples were screened using Luminex arrays that included 58 cytokines and 55 autoantigens, many of which are associated with connective tissue diseases (CTDs). Samples positive for anti-cytokine antibodies were tested for receptor blocking activity using cell-based functional assays. Anti-cytokine antibodies were identified in > 50% of patients across all 5 acutely ill cohorts. In critically ill patients, anti-cytokine antibodies were far more common in infected versus uninfected patients. In cell-based functional assays, 11 of 39 samples positive for select anti-cytokine antibodies displayed receptor blocking activity against surface receptors for Type I IFN, GM-CSF, and IL-6. Autoantibodies against CTD-associated autoantigens were also commonly observed, including newly detected antibodies that emerged in longitudinal samples. These findings demonstrate that anti-cytokine and autoantibodies are common across different viral and nonviral infections and range in severity of illness.
ABSTRACT Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines ...is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as “souring”) is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.
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