Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis

The impact of DNA extraction protocol on soil DNA yield and bacterial community composition was evaluated. Three different procedures to physically disrupt cells were compared: sonication, grinding-freezing-thawing, and bead beating. The three protocols were applied to three different topsoils. For all soils, we found that each DNA extraction method resulted in unique community patterns as measured by denaturing gradient gel electrophoresis. This indicates the importance of the DNA extraction protocol on data for evaluating soil bacterial diversity. Consistently, the bead-beating procedure gave rise to the highest number of DNA bands, indicating the highest number of bacterial species. Supplementing the bead-beating procedure with additional cell-rupture steps generally did not change the bacterial community profile. The same consistency was not observed when evaluating the efficiency of the different methods on soil DNA yield. This parameter depended on soil type. The DNA size was of highest molecular weight with the sonication and grinding-freezing-thawing procedures (approx. 20 kb). In contrast, the inclusion of bead beating resulted in more sheared DNA (approx. 6-20 kb), and the longer the bead-beating time, the higher the fraction of low-molecular weight DNA. Clearly, the choice of DNA extraction protocol depends on soil type. We found, however, that for the analysis of indigenous soil bacterial communities the bead-beating procedure was appropriate because it is fast, reproducible, and gives very pure DNA of relatively high molecular weight. And very importantly, with this protocol the highest soil bacterial diversity was obtained. We believe that the choice of DNA extraction protocol will influence not only the determined phylogenetic diversity of indigenous microbial communities, but also the obtained functional diversity. This means that the detected presence of a functional gene—and thus the indication of enzyme activity—may depend on the nature of the applied DNA extraction procedure.     

Soil organic carbon and nitrogen in aggregates in response to over seven decades of farmyard manure application

The study aimed to evaluate the effects of long-term fertilisation on soil aggregation and the associated changes in soil organic carbon (SOC) and nitrogen (N) pools in aggregates. The combined application of mineral fertiliser and manure improved soil aggregation, SOC and N content in aggregates, compared to manure or mineral fertiliser alone, and thus proved to be a suitable fertilisation strategy to increase C sequestration in agroecosystems.     

Detection by real-time quaking-induced conversion (RT-QuIC), ELISA,and IHC of chronic wasting disease prion in lymph nodes from Pennsylvania white-tailed deer with specific PRNP genotypes

Chronic wasting disease (CWD) is a prion-mediated, transmissible disease of cervids, including deer (Odocoileus spp.), which is characterized by spongiform encephalopathy and death of the prion-infected animals. Official surveillance in the United States using immunohistochemistry (IHC) and ELISA entails the laborious collection of lymphoid and/or brainstem tissue after death. New, highly sensitive prion detection methods, such as real-time quaking-induced conversion (RT-QuIC), have shown promise in detecting abnormal prions from both antemortem and postmortem specimens. We compared RT-QuIC with ELISA and IHC for CWD detection utilizing deer retropharyngeal lymph node (RLN) tissues in a diagnostic laboratory setting. The RLNs were collected postmortem from hunter-harvested animals. RT-QuIC showed 100% sensitivity and specificity for 50 deer RLN (35 positive by both IHC and ELISA, 15 negative) included in our study. All deer were also genotyped for PRNP polymorphism. Most deer were homozygous at codons 95, 96, 116, and 226 (QQ/GG/AA/QQ genotype, with frequency 0.86), which are the codons implicated in disease susceptibility. Heterozygosity was noticed in Pennsylvania deer, albeit at a very low frequency, for codons 95GS (0.06) and 96QH (0.08), but deer with these genotypes were still found to be CWD prion-infected.     

Impact of a reduced water salinity on the composition of Vibrio spp. in recirculating aquaculture systems for Pacific white shrimp (Litopenaeus vannamei) and its possible risks for shrimp health and food safety

Tropical shrimp, like Litopenaeus vannamei, in land‐based recirculating aquaculture systems (RAS) are often kept at low water salinities to reduce costs for artificial sea salt and the amount of salty wastewater. Although these shrimp are tolerant against low salinities, innate immunity suppression and changes in the microbial composition in the water can occur. As especially Vibrio spp. are relevant for shrimp health, alterations in the species composition of the Vibrio community were analysed in water from six RAS, run at 15‰ or 30‰. Additionally, pathogenicity factors including pirA/B, VPI, toxR, toxS, vhh, vfh, tdh, trh, flagellin genes and T6SS1/2 of V. parahaemolyticus were analysed. The Vibrio composition differed significantly depending on water salinity. In RAS at 15‰, higher numbers of the potentially pathogenic species V. parahaemolyticus, V. owensii and V. campbellii were detected, and especially in V. parahaemolyticus, various pathogenicity factors were present. A reduced salinity may therefore pose a higher risk of disease outbreaks in shrimp RAS. Because some of the detected pathogenicity factors are relevant for human health, this might also affect food safety. In order to produce healthy shrimp as a safe food for human consumption, maintaining high water salinities seems to be recommendable.     

A method for applying fluvial geomorphology in support of catchment‐scale river restoration planning

• 1. This paper reports on an extension to the use of Fluvial Audit survey to include a subjective and adaptive multi‐criteria assessment (MCA) process that integrates scientific literature and observational data to develop three reach‐scale indices of: (a) channel modification; (b) channel function (sediment store or source); and (c) naturalness. These indices are nested within an overall conceptual model of channel evolution and used to underpin catchment scale river restoration.
• 2. The approach is described and applied to a small groundwater dominated river in the UK. The results show that over 48% of the total main river was in a degraded state relative to a conceptual model of a natural reference state. Only 23% of the river was in a near‐natural state.
• 3. MCA classifications were translated into a set of management actions necessary to return each reach to a near‐natural condition. These are described.
• 4. The method offers a transparent decision support for stakeholders that can incorporate differing scientific evidence. The use of MCA enables flexibility in terms of the relative importance of scores and weights placed upon factors in the final classification. This makes the approach amenable to stakeholder and public consultation.

Copyright © 2009 John Wiley & Sons, Ltd.     

Monitoring infection with Piscine myocarditis virus and development of cardiomyopathy syndrome in farmed Atlantic salmon (Salmo salar L.) in Norway

An epidemiological study was carried out in Norway in 2015–2018, investigating the development of infection with Piscine myocarditis virus (PMCV) and development of cardiomyopathy syndrome (CMS) in farmed Atlantic salmon. Cohorts from 12 sites were followed and sampled every month or every other month from sea transfer to slaughter. PMCV was detected at all sites and in all sampled cages, and fish in six sites developed clinical CMS. The initial infection happened between 1 and 7 months post‐sea transfer, and the median time from infection with PMCV until outbreak of CMS was 6.5 months. Generally, fish from sites with CMS had higher viral titre and a higher prevalence of PMCV, compared to sites that did not develop clinical CMS. The virus persisted until the point of slaughter at most (11 out of 12) of the sites. The detection of PMCV in all sites suggests that PMCV is more widespread than previously known. Screening for PMCV as a tool to monitor impending outbreaks of CMS must be supported by observations of the health status of the fish and risk factors for development of disease.     

Early effects of COVID‐19 on US fisheries and seafood consumption

The US seafood sector is susceptible to shocks, both because of the seasonal nature of many of its domestic fisheries and its global position as a top importer and exporter of seafood. However, many data sets that could inform science and policy during an emerging event do not exist or are only released months or years later. Here, we synthesize multiple data sources from across the seafood supply chain, including unconventional real‐time data sets, to show the relative initial responses and indicators of recovery during the COVID‐19 pandemic. We synthesized news articles from January to September 2020 that reported effects of COVID‐19 on the US seafood sector, including processor closures, shortened fishing seasons and loss of revenue. Concerning production and distribution, we assessed past and present landings and trade data and found substantial declines in fresh seafood catches (?40%), imports (?37%) and exports (?43%) relative to the previous year, while frozen seafood products were generally less affected. Google search trends and seafood market foot traffic data suggest consumer demand for seafood from restaurants dropped by upwards of 70% during lockdowns, with recovery varying by state. However, these declines were partially offset by an increase (270%) in delivery and takeout service searches. Our synthesis of open‐access data sets and media reports shows widespread, but heterogeneous, ramifications of COVID‐19 across the seafood sector, implying that policymakers should focus support on states and sub‐sectors most affected by the pandemic: fishery‐dependent communities, processors, and fisheries and aquaculture that focus on fresh products.     

Word learning in a domestic dog: evidence for "fast mapping"

During speech acquisition, children form quick and rough hypotheses about the meaning of a new word after only a single exposure-a process dubbed "fast mapping." Here we provide evidence that a border collie, Rico, is able to fast map. Rico knew the labels of over 200 different items. He inferred the names of novel items by exclusion learning and correctly retrieved those items right away as well as 4 weeks after the initial exposure. Fast mapping thus appears to be mediated by general learning and memory mechanisms also found in other animals and not by a language acquisition device that is special to humans.     

Something old,something new: Historical perspectives provide lessons for blue growth agendas

The concept of “blue growth,” which aims to promote the growth of ocean economies while holistically managing marine socioecological systems, is emerging within national and international marine policy. The concept is often promoted as being novel; however, we show that historical analogies exist that can provide insights for contemporary planning and implementation of blue growth. Using a case‐study approach based on expert knowledge, we identified 20 historical fisheries or aquaculture examples from 13 countries, spanning the last 40–800 years, that we contend embody blue growth concepts. This is the first time, to our knowledge, that blue growth has been investigated across such broad spatial and temporal scales. The past societies managed to balance exploitation with equitable access, ecological integrity and/or economic growth for varying periods of time. Four main trajectories existed that led to the success or failure of blue growth. Success was linked to equitable rather than open access, innovation and management that was responsive, holistic and based on scientific knowledge and monitoring. The inability to achieve or maintain blue growth resulted from failures to address limits to industry growth and/or anticipate the impacts of adverse extrinsic events and drivers (e.g. changes in international markets, war), the prioritization of short‐term gains over long‐term sustainability, and loss of supporting systems. Fourteen cross‐cutting lessons and 10 recommendations were derived that can improve understanding and implementation of blue growth. Despite the contemporary literature broadly supporting our findings, these recommendations are not adequately addressed by agendas seeking to realize blue growth.     

Integrated pest management and weed management in the United States and Canada

There is interest in more diverse weed management tactics because of evolved herbicide resistance in important weeds in many US and Canadian crop systems. While herbicide resistance in weeds is not new, the issue has become critical because of the adoption of simple, convenient and inexpensive crop systems based on genetically engineered glyphosate‐tolerant crop cultivars. Importantly, genetic engineering has not been a factor in rice and wheat, two globally important food crops. There are many tactics that help to mitigate herbicide resistance in weeds and should be widely adopted. Evolved herbicide resistance in key weeds has influenced a limited number of growers to include a more diverse suite of tactics to supplement existing herbicidal tactics. Most growers still emphasize herbicides, often to the exclusion of alternative tactics. Application of integrated pest management for weeds is better characterized as integrated weed management, and more typically integrated herbicide management. However, adoption of diverse weed management tactics is limited. Modifying herbicide use will not solve herbicide resistance in weeds, and the relief provided by different herbicide use practices is generally short‐lived at best. More diversity of tactics for weed management must be incorporated in crop systems. © 2014 Society of Chemical Industry