Microbial community responses associated with the development of oomycete plant pathogens on tomato roots in soilless growing systems

AIMS: To determine the spread of different oomycete pathogens in hydroponic, soilless tomato growing systems and their impact on established microbial communities, as baseline studies prior to future introduction of microbial inoculants for disease suppression. METHODS AND RESULTS: The oomycete pathogens, Pythium group F, Pythium aphanidermatum and Phytophthora cryptogea, were introduced into small-scale recirculating tomato growing systems containing rockwool 6 weeks after set-up when roots were well-established. Two weeks later, half of the systems were switched over to run-to-waste. Pythium aphanidermatum spreads the fastest, Pythium group F the slowest and Ph. cryptogea was intermediate in its spread. The switch to run-to-waste had no effect on pathogen recovery. Microbial communities, monitored by dilution plating, were well-established at the first sampling, 6 weeks after set-up and although differences in community levels were found between experiments, changes during any one experiment were small, generally less than 1 log10 CFU g(-1) for bacteria. Pathogen introduction increased microbial community levels in roots but the switch to run-to-waste had no effect. Analysis of bacterial communities through amplification of a fragment of the 16S rRNA gene and DGGE profiling showed that different communities were established within each pathogen experiment and that different communities were established on roots, rockwool and in nutrient solutions. However, no significant changes in microbial profiles were found over time in any experiment. CONCLUSIONS: In these systems, the microbial communities were well-established 6 weeks after set-up and were resistant to biological and physical perturbation. SIGNIFICANCE AND IMPACT OF THE STUDY: The implication for microbial inoculation of such systems for disease suppression is that the micro-organisms would either have to be introduced very early during the set-up of the system or be able to replace an established but variable community.     

Comparison of intrinsic dynamics of cytochrome p450 proteins using normal mode analysis

Cytochrome P450 enzymes are hemeproteins that catalyze the monooxygenation of a wide‐range of structurally diverse substrates of endogenous and exogenous origin. These heme monooxygenases receive electrons from NADH/NADPH via electron transfer proteins. The cytochrome P450 enzymes, which constitute a diverse superfamily of more than 8,700 proteins, share a common tertiary fold but < 25% sequence identity. Based on their electron transfer protein partner, cytochrome P450 proteins are classified into six broad classes. Traditional methods of protein classification are based on the canonical paradigm that attributes proteins’ function to their three‐dimensional structure, which is determined by their primary structure that is the amino acid sequence. It is increasingly recognized that protein dynamics play an important role in molecular recognition and catalytic activity. As the mobility of a protein is an intrinsic property that is encrypted in its primary structure, we examined if different classes of cytochrome P450 enzymes display any unique patterns of intrinsic mobility. Normal mode analysis was performed to characterize the intrinsic dynamics of five classes of cytochrome P450 proteins. The present study revealed that cytochrome P450 enzymes share a strong dynamic similarity (root mean squared inner product > 55% and Bhattacharyya coefficient > 80%), despite the low sequence identity (< 25%) and sequence similarity (< 50%) across the cytochrome P450 superfamily. Noticeable differences in C_α atom fluctuations of structural elements responsible for substrate binding were noticed. These differences in residue fluctuations might be crucial for substrate selectivity in these enzymes.     

Peracetic acid activity on biofilm formed by Escherichia coli isolated from an industrial water system

One of the major problems in industrial water systems is the generation of biofilm, which is resistant to antimicrobial agents and causes failure of sanitization policy. This work aimed to study the anti-biofilm activity of peracetic acid (PAA) at contact times and temperatures combinations. To this end, a 96-well microtiter-based calorimetric method was applied in in vitro biofilm production using Escherichia coli, isolated from the water supply system of a pharmaceutical plant. The phenotypic and phylogenetic tests confirmed that the isolated bacteria belong to strains of Escherichia coli. The anti-biofilm activity of peracetic acid on formed biofilm was investigated at concentrations of 0·15–0·5% for a contact time of 5–15 min at 20–60°C. The maximum biofilm formation by MTP method using an Escherichia coli isolate was achieved in 96-h incubation in TSB containing wells at 37°C. Biofilm formation rate shown to be high by the environmental isolate compared with that of standard strain. PAA at concentrations above 0·25%, the temperature of 40°C and a minimum of 10 min of contact time was effective in the eradication of biofilm in an MTP-based system.     

Toward a universal measure of robustness across model organs and systems

The development of an individual must be capable of resisting the harmful effects of internal and external perturbations. This capacity, called robustness, can make the difference between normal variation and disease. Some systems and organs are more resilient in their capacity to correct the effects of internal disturbances such as mutations. Similarly, organs and organisms differ in their capacity to be resilient against external disturbances, such as changes in temperature. Furthermore, all developmental systems must be somewhat flexible to permit evolutionary change, and understanding robustness requires a comparative framework. Over the last decades, most research on developmental robustness has been focusing on specific model systems and organs. Hence, we lack tools that would allow cross-species and cross-organ comparisons. Here, we emphasize the need for a uniform framework to experimentally test and quantify robustness across study systems and suggest that the analysis of fluctuating asymmetry might be a powerful proxy to do so. Such a comparative framework will ultimately help to resolve why and how organs of the same and different species differ in their sensitivity to internal (e.g., mutations) and external (e.g., temperature) perturbations and at what level of biological organization buffering capacities exist and therefore create robustness of the developmental system.     

The impact of work organisation on the work life of people on pasture-based dairy farms

The seasonal workload combined with increased dairy herd sizes and a declining workforce have created social sustainability challenges for pasture-based dairy farms. Effective work organisation can build productive capacity that may have a positive impact on this scenario. Our objective was to develop a framework to characterise and examine the effect of work organisation on the working situations of the people involved in a sample of 55 pasture-based dairy farms in Ireland. We conceptualised that effective work organisation on a dairy farm could be considered as a system that is efficient from a labour input perspective, resulting in a profitable farming system with outcomes of good operator well-being, health and safety, and quality of life. A literature review established efficiency & productivity, flexibility and standardisation as our three characteristics of work organisation. Using data from an existing labour time-use study completed from the 1st February to 30th June 2019, we aimed to test the veracity of these work organisation characteristics in the Irish pasture-based dairy system. Two proxy indicators were selected to represent each of the three work organisation characteristics, and each of the 55 farms were categorised into quartiles based on their ranking for these six indicators (1 = most effective quartile to 4 = least effective quartile). The most and least effective quartiles of farms for work organisation showed similar levels of farm labour input and labour efficiency. Farmers in the most effective work organisation quartile were working 51.2 h/week from February to June compared with 70.0 h/week for farmers in the least effective quartile, which was attributed to later start times, earlier finish times, and more time at non-farm activity. Farms achieving effective work organisation had a labour-efficient system with relatively low farmer working hours. Extension of the work organisation concept to other farms could improve their labour situation and aid in alleviating some of the key quality of life challenges faced by dairy farmers.     

A functional trait framework for integrating nitrogen-fixing cover crops into short-rotation woody crop systems

Developing approaches to simultaneously maximize short-rotation woody crop (SRWC) productivity while minimizing footprints associated with intensive management is imperative to profitable and sustainable bioenergy production systems. Intercropping nitrogen (N)-fixing cover crops in SRWC systems is an overlooked approach to sustainably intensify SRWC production by increasing N availability using less environmentally costly inputs. Here, we discuss how functional traits (e.g., seasonal activity, lifespan, leaf habit, soil exploration) of cover crops and SRWCs may interact through space and time influencing access to light, water, and nutrients to provide a framework for successful integration of cover crops into SRWCs. Next, we summarize the literature on intercropping forest plantations with N-fixing cover crops to identity research gaps and outline future research needs and opportunities. And then, using empirical N demand and productivity data from SRWCs and cover crop N inputs from the literature, we illustrate how SRWC leaf habit (conifer evergreens and deciduous hardwoods) would influence successful integration of cover crops and potential N fixation. We estimate that integrating cover crops into SRWCs could supply 27% and 72% of the N demand across a 10-year rotation for an evergreen and a deciduous hardwood, respectively. These figures suggest these integrated SRWC systems may approach a virtual minimal external N input when other biogeochemical cycles are considered. The guiding principles presented here are grounded in ecological theory and provide a framework for sustainable intensification of forest production.     

Respiration cycle duration and seawater flux through open blowholes of humpback (Megaptera novaeangliae) and North Atlantic right (Eubalaena glacialis) whales

Little is known about the dynamics of baleen whale respiratory cycles, especially the mechanics and activity of the blowholes and their interaction with seawater. In this study, the duration of complete respiration cycles (expiration/inhalation events) were quantified for the first time in two species: North Atlantic right whale (NARW) and humpback whale (HW) using high resolution, detailed imagery from an unoccupied aerial system (UAS). The mean duration of complete respiration cycles (expiration/inhalation event) in the NARW and HW were 3.07 s (SD = 0.503, n = 15) and 2.85 s (SD = 0.581, n = 21), respectively. Furthermore, we saw no significant differences in respiration cycle duration between age and sex classes in the NARW, but significant differences were observed between age classes in the HW. The observation of seawater covering an open blowhole was also quantified, with NARW having 20% of all breaths with seawater presence versus 90% in HW. Seawater incursion has not been described previously and challenges the general consensus that water does not enter the respiratory tract in baleen whales. Prevalent seawater has implications for the analysis and interpretation of exhaled respiratory vapor/mucosa samples, as well as for the potential inhalation of oil in spills.