Find research datasets worth reusing

opencc-zeroFeb 2023View details →

Using standardized fish-specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities

1. Biodiversity inventories and monitoring techniques for marine fishes often overlook small (<5cm), bottom-associated ('cryptobenthic') fishes, and few standardized, comparative assessments of cryptobenthic fish communities exist. We sought to develop a standardized, quantitative survey method for cryptobenthic fishes that permits their sampling across a variety of habitats and conditions. 2. Fish-specific autonomous reef monitoring structures (FARMS) are designed to sample cryptobenthic fishes using a suite of accessible and affordable materials. To generate a variety of microhabitats, FARMS consist of three layers of stacked PVC pipes in three different sizes, as well as a bottom and top level of loose PVC-pipe fragments in a mesh basket. We deployed FARMS across a variety of habitats, including coral reefs, seagrass beds, oyster reefs, mangroves, and soft-bottom habitats across six locations (Hawai'i, Texas, Panama, Saudi Arabia, Brazil, and Curaçao). 3. From shallow estuaries to coral reefs beyond 100 m depth, FARMS attracted distinct communities of native cryptobenthic fishes with strong site or habitat specificity. Comparing the FARMS to communities sampled with alternative methods (enclosed clove-oil stations on coral reefs in Panama and oyster sampling units on oyster reefs in Texas) suggests that FARMS yield a subset of cryptobenthic species representative of those present on local coral and oyster reefs. While FARMS yield fewer individuals per sample and are restricted to cryptobenthic species, they are efficient sampling devices relative to the sampled area. 4. We demonstrate that FARMS represent a useful tool for standardized collections of cryptobenthic fishes. While natural substrata are bound to yield more mature communities with a larger number of individuals and wider range of specialist species, the potential to deploy and retrieve FARMS in turbid environments, beyond regular SCUBA depth, and where fish collections using anesthetics or ichthyocides are forbidden suggests that they are a valuable complementary technique to survey fishes in aquatic ecosystems. Deploying FARMS in locations and habitats where cryptobenthic fish communities have not been studied in detail may yield many valuable specimens of unknown or poorly known species.

opencc-zeroMar 2023View details →

Data for: Avian use of avocado farms and intact forest in the northern Sierra de Bahoruco, Dominican Repebulic

The Dominican Republic is experiencing increased forest loss due to the expansion of avocado farming. While agricultural lands can provide viable habitat for birds, knowledge of avian use of avocado farms relative to native forest is limited. We conducted surveys in fall 2021 to compare the bird communities and vegetation complexity of two avocado farm sites and two native dry forest sites in the northern Sierra de Bahoruco region of the Dominican Republic to assess avian habitat use. Overall, we found that habitat associations differed for bird species distinguished by contrasting geographic ranges. In particular, the abundance, richness, and diversity of bird species endemic to Hispaniola were significantly greater in forests than in farms, while non-endemic resident bird species had the opposite habitat associations. The abundance, richness, and diversity of Neotropical migrants exhibited fewer distinct differences between farm and forest sites. Vegetation structural complexity was reduced in avocado farms relative to forests and was positively associated with the abundance, richness, and diversity of endemic bird species but negatively associated with these community measures of non-endemic resident species. Collectively, our findings suggest that avocado farms could provide viable habitat for non-endemic resident and migrant bird species, but that endemic species could be negatively impacted by an increase in avocado farming in the region. We offer recommendations for forest preservation, farming practices, and future research that could help to inform the conservation of endemic species in the region.

opencc-by-4.0Dec 2022View details →

Goat milk microbiota of Dutch farms

Microbiota composition of raw milk in relation to Dutch goat farm management. After amplicon sequencing we analyzed the taxa at phylum and genus levels. On ten farms our results indicated that the number of microbiota composition of the milk, directly after milking was variable among farms and not related to the farm management system. The milk microbiota showed a farm-specific fingerprint. Repeated sampling of a farm showed that this fingerprint changed over time. The lactic acid producing bacteria showed a similar pattern. Variable microbiota richness amount and diversity of microorganisms were present in different farming systems. We concluded that farm-specific management and sampling moment were the major determining factors for the milk microbiota composition.

opencc-zeroMar 2023View details →

Intensified livestock farming increases antibiotic resistance genotypes and phenotypes in animal feces

Animal feces from livestock farming can be a major source of antibiotic resistance to the environment, but a clear gap exists on how the resistance reservoir in feces alters as farming activities intensify. Here, we sampled feces from eight Chinese farms, where yak, sheep, pig, and horse were reared under free-range to intensive conditions, and determined fecal resistance using both genotype and phenotype approaches. Animals reared intensively exhibited increased diversity of antibiotic resistance genes (ARGs) and greater resistance phenotypes in feces, which were cross-correlated. Furthermore, at the metagenome contig level, ARGs were co-located with mobile genetic elements at a higher frequency (27.38%) as farming intensified, with associated resistance phenotypes being less coupled with bacterial phylogeny. Intensified farming also expanded the multidrug resistance preferentially carried on pathogens in fecal microbiomes. Overall, farming intensification can increase antibiotic resistance genotypes and phenotypes in domestic animal feces, with implications for environmental health.

Raw_data_Combining several indicators to assess the effectiveness of tailor-made health plans in pig farms

Raw data for a paper submitted to Peer Community In Animal Science.

Figures: The wind farm as a sensor: learning and explaining orographic and plant-induced flow heterogeneities from operational data

Python figures in pickle format matplotlib version 3.5.1

opencc-zeroMar 2023View details →

FIG. 2 in First in situ middle Pliocene cercopithecoid fossils from the Palaeokarst System of Bolt's Farm (South Africa)

FIG. 2. — View of the locus BPB with the "Parapapio spot" in the white circle.

opencc-zeroApr 2023View details →

Fencing farm dams to exclude livestock halves methane emissions and improves water quality

Agricultural practices have created tens of millions of small artificial water bodies ("farm dams" or "agricultural ponds") to provide water for domestic livestock worldwide. Among freshwater ecosystems, farm dams have some of the highest greenhouse gas (GHG) emissions per m2 due to fertilizer and manure run-off boosting methane production – an extremely potent GHG. However, management strategies to mitigate the substantial emissions from millions of farm dams remain unexplored. We tested the hypothesis that installing fences to exclude livestock could reduce nutrients, improve water quality, and lower aquatic GHG emissions. We established a large-scale experiment spanning 400 km across south-eastern Australia where we compared unfenced (N = 33) and fenced farm dams (N = 31) within 17 livestock farms. Fenced farm dams recorded 32% less dissolved nitrogen, 39% less dissolved phosphorus, 22% more dissolved oxygen, and produced 56% less diffusive methane emissions than unfenced dams. We found no effect of farm dam management on diffusive carbon dioxide emissions and on the organic carbon in the soil. Dissolved oxygen was the most important variable explaining changes in carbon fluxes across dams, whereby doubling dissolved oxygen from 5 to 10 mg L-1 led to a 74% decrease in methane fluxes, a 124% decrease in carbon dioxide fluxes, and a 96% decrease in CO2-eq (CH4 + CO2) fluxes. Dams with very high dissolved oxygen (>10 mg L-1) showed a switch from positive to negative CO2-eq. (CO2 + CH4) fluxes (i.e., negative radiative balance), indicating a positive contribution to reducing atmospheric warming. Our results demonstrate that simple management actions can dramatically improve water quality and decrease methane emissions while contributing to more productive and sustainable farming.

opencc-by-4.0Apr 2023View details →

Wind Farm Survey Ireland 2019

A survey of windfarms in Ireland as of 2019 as part of my introductory period in my PhD research at the University of Limerick funded by Sustainable Energy Authority of Ireland.

opencc-zeroApr 2023View details →

Data and codes from: Taxon-specific responses to landscape-scale and long-term implementation of environmentally friendly rice farming

<ol> <li> Rice feeds about half of the world's population. The intensification of rice farming has threatened biodiversity and ecosystem services, such as pest control. A growing body of evidence suggests that environmentally friendly rice farming (EFF) can be effective in biodiversity conservation. However, its dependence on spatial and temporal scales of EFF implementation and surrounding seminatural habitats has remained largely unknown. </li> <li> We evaluated the effects of three types of EFF (organic farming, winter flooding and Integrated Pest Management [IPM]) against conventional farming on plants, spiders, and waterbirds in Japan. Through systematic surveys of 254 rice fields across rice production areas, we monitored EFF implementation at field and landscape scales, considering the time since transition to EFF and the surrounding seminatural areas. </li> <li> EFF implementation at the field scale, such as organic farming, was found to have positive effects on plant richness and spider abundance, whereas the percent area of EFF fields within a 200-m radius positively affected Ardeidae abundance. However, as the percent area of surrounding semi-natural habitats increased, the difference in the plant richness between organic and other fields decreased. </li> <li>Prolonged implementation periods of IPM or winter flooding, together with a reduction of more than 50% in synthetic fertilisers and pesticides from conventional agriculture, led to an increase in the spider abundance. Conversely, no clear positive effect of longer implementation periods of organic farming resulted in similar spider abundance in the three EFF types after 20 years.</li> <li> Synthesis and applications. This suggests that the benefits of environmentally friendly rice farming depend on their spatial and temporal scales and the surrounding seminatural areas. We propose that such a context dependency should be considered in future policy. Our findings also provide a starting point for future research to test the mixed biodiversity benefits of EFF across cropland types and around the world. </li> </ol>

opencc-by-4.0Apr 2023View details →

Occupational Hazards of Indian Shrimp Farm Workers

The paper reviews a range of global aquaculture health and safety literature to inform and contribute to the development of a socio-economic profile of Indian shrimp farm workers including the occupational hazards and injuries they face. In addition, sixty shrimp farm workers were interviewed from each of the states of Andhra Pradesh, Maharashtra, Gujarat and Tamil Nadu. The study revealed that all shrimp farm workers were male, 58% were migrants, and ages ranged from 23-53 years with work experience of 5-24 years. Few workers (14%) had no formal schooling and many had secondary level education. Reported physical hazards were high (93%) followed by biological (82%), chemical (77%), ergonomic (71%) and psycho-social (71%) hazards. The majority of physical injuries reported related to slips, falls and cuts (51%), electric shocks (44%), sunburn (41%), dehydration/headaches (40%) and fractures (27%). Approximately 30 to 39% had some chemical injury with skin infections/breathing problems. Indian shrimp farm workers face similar occupational hazards and injuries to shrimp farm workers in other countries. The occupational health and safety of shrimp farm workers should be integrated into the concept of ‘One Health’ to ensure aquaculture sustainability and safe, meaningful and good quality employment to workers.

opencc-by-4.0May 2023View details →

European offshore wind farms and marine energy deployements

Three distinct dataset used to forecast the development of marine energy in Europe in the upcoming three decades: - European offshore wind farms - tidal energy converter deployements in Europe - wave energy converter deployements in Europe

A Comparison of Passive and Active Dust Sampling Methods for Measuring Airborne MRSA in Pig Farms

Study Abstract: Authors: Anne Rittscher, Abel A. Vlasblom, Birgitta Duim, Peter Scherpenisse, Isabella van Schothorst, Inge M. Wouters, Liese Van Gompel, Lidwien A.M. Smit      Methicillin resistant strains of Staphylococcus aureus (MRSA) are resistant to most b-lactam antibiotics. Pigs are an important reservoir of livestock associated MRSA (LA-MRSA), which is genetically distinct from both hospital and community acquired MRSA. Occupational exposure to pigs on farms can lead to LA-MRSA carriage by workers. There is a growing body of research on MRSA found in the farm environment, the airborne route of transmission, and its implication on human health. This study aims to compare two sampling methods used to measure airborne MRSA in the farm environment; passive dust sampling with electrostatic dust fall collectors (EDCs), and active inhalable dust sampling using stationary air pumps with Teflon filters. Paired dust samples using  EDCs and GSP samplers, totaling 87 samples, were taken from seven Dutch pig farms, in multiple compartments housing pigs of varying ages. Total nucleic acids of both types of dust samples were extracted and targets indicating MRSA (femA, nuc, mecA) and total bacterial count (16S rRNA) were quantified using quantitative Real Time PCRs. MRSA could be measured in all stationary pump samples and in 94% of the EDCs, additionally MRSA was present on every farm sampled. There was a strong positive relationship between the paired MRSA levels found in EDCs and those measured on filters (Normalized by 16S rRNA; Pearson’s correlation coefficient r=0.94, Not Normalized; Pearson’s correlation coefficient r=0.84). This study suggests that EDCs can be used as an affordable and easily standardized method for quantifying airborne MRSA levels in the pig farm setting.

opencc-by-4.0May 2023View details →

A stratified compartmental model for the transmission of Sparicotyle chrysophrii (Platyhelminthes: Monogenea) in gilthead seabream (Sparus aurata) fish farms

This repository hosts data and model codes of the paper: "A stratified compartmental model for the transmission of Sparicotyle chrysophrii (Platyhelminthes: Monogenea) in gilthead seabream (Sparus aurata) fish farms"  by Stella et al., Royal Society Open Science, 2023. doi:https://doi.org/10.1098/rsos.221377 Programming Language: MatLab The code has been tested on Matlab R2019b. Run the Main_Sparicotyle.m file code to reproduce Figures 2, 3, and 5 to 9 of the paper.

opencc-zeroJun 2023View details →

Reversing declines in farmland birds: how much agri-environment provision is needed at farm and landscapes scales?

1) Agri-environment schemes (AES) are the primary policy mechanism for addressing farmland biodiversity declines across Europe. Despite previous studies on the impacts of AES on biodiversity, there is little empirical evidence on the scale of provision required to reverse declines. 2) Across three regions of lowland England with contrasting farm systems (arable, pastoral, mixed) we estimated avian Population Growth Rates (PGRs) on farmland with high AES provision ('higher-tier': average bird-friendly option cover = 7.4%), low AES provision ('lower-tier': 2.3%), and no bird-friendly AES ('no AES'). Ten-year PGRs were derived for 24 species and three multi-species groups comprising farmland-associated species ('farmland birds'), species of conservation concern ('priority birds'), and species restricted to farmland ('specialist birds'). We used PGRs to simulate the proportion of the regional farmland landscape that would have to be assigned to higher- and lower-tier agreements to stabilise or increase populations. 3) In the arable and pastoral regions, 13/23 and 13/22 species respectively had more positive PGRs under higher-tier AES than on no AES farmland (none had more negative PGRs), compared to 4/22 (positive) and 1/22 (negative) in the mixed region. Only 2-4 species per region exhibited more positive PGRs under lower-tier AES compared to no AES farmland. 4) Multi-species PGRs in the arable and pastoral regions increased from no AES (strong decline), to lower-tier (decline or stability) to higher-tier (moderate or strong increase). There was no overall AES effect in the mixed region. 5) To increase regional farmland bird populations by 10% over 10-years, 47% and 26% of the farmed landscape would need to be devoted to higher-tier agreements in arable and pastoral landscapes respectively. This falls to 34% and 17% when higher-tier is targeted at localities supporting higher abundances of target species, and to 29% and 10% when 30% of the farmed landscape is also devoted to lower-tier. Priority and specialist birds require higher provision levels. 6) Policy implications. Where farmland bird recovery is an AES objective, farms should prioritise higher-tier agreement delivery over lower-tier. Farmland bird responses to AES provision are likely to vary regionally but careful targeting will reduce the amount needed in the landscape.

opencc-by-4.0Jun 2023View details →

Techno-economic evaluation and resource assessment of hydrogen production through offshore wind farms: A European perspective - Supplementary material

This is the additional material provided with the journal article "Techno-economic evaluation and resource assessment of hydrogen production through offshore wind farms:  A European perspective" published in Renewable and Sustainable Energy Reviews (<a href="https://doi.org/10.1016/j.rser.2023.113699">https://doi.org/10.1016/j.rser.2023.113699</a>). Datasets are provided as NetCDF files for European maps and CSVfor Economically Attractive Resource curves. European and National plots are provided as PDF files.

Shellfish aquaculture farms as foraging habitat for nearshore fishes and crabs

This is the dataset used for the analysis in our paper. The file contains species counts and behavior classifications of nearshore fish and crabs taken from time-lapse underwater video. Also included are habitat transect data from each site. Presence/absence of zostera marina and zostera japonica eelgrass, algae, as well as eelgrass metrics were quantified in the transects. The metadata spreadsheet contains descriptions of each column in the datasheet. This data was collected at shellfish aquaculture farm sites across Puget Sound, Washington, USA in 2017, 2018, and 2019 using underwater timelapse video cameras and habitat transects. Transects were done with 1/4 meter^2 quadrat divided into 25 10x10cm^2 squares, each quadrat was measured 5 times along a 30 meter line parallel to shore. Video was recorded in 2 minute lengths every 10 minutes starting 1 hour before high tide, going to 1 hour after high tide, using cameras positioned approximately 18 inches off the substrate. PVC stakes were used to mark a 1 meter square of camera visibility and organisms observed within that 1 meter square were recorded.  For more information, see my chapter 1 thesis.

opencc-zeroJun 2023View details →

Data from: Pest management science often disregards farming system complexities

Since the 1940s, pesticide-intensive crop protection has sustained food security but also caused pervasive impacts on biodiversity, environmental integrity and human health. Here, we employ a systematic literature review to structurally analyze pest management science in 65 developing countries. Within a corpus of 3,407 publications, we find that taxonomic coverage is skewed towards a subset of 48 herbivores. Simplified contexts are commonplace: 48% of studies are performed within laboratory confines. 80% treat management tactics in an isolated rather than integrated fashion. 83% consider no more than two out of 15 farming system variables. Limited attention is devoted to pest-pathogen or pest-pollinator interplay, trophic interactions across ecosystem compartments or natural pest regulation. By overlooking social strata, the sizable scientific progress on agroecological management translates into slow farm-level uptake. We argue that the scientific enterprise should integrate system complexity to chart sustainable trajectories for global agriculture and achieve transformative change on the ground.

opencc-zeroJun 2023View details →

Transition to organic farming negatively affects bat activity

<ol> <li>The effectiveness of organic farming on biodiversity has been widely documented especially for plants, arthropods and birds; however, the effects of the transition period required to become an organic farm on wildlife remain poorly understood.</li> <li>We assessed the effects of organic farming on insectivorous bats in citrus orchards in the Republic of Cyprus employing two matched designs (conventional vs. 3-years organic-transitional and conventional vs. organic-certified) and a third unmatched design (3-years organic-transitional vs. organic-certified). We specifically investigated whether the transition period prior to full organic certification influenced bat activity with a special focus on any moderation effects from surrounding semi-natural areas.</li> <li>The activity of three (Pipistrellus kuhlii, Hypsugo savii and Miniopterus schreibersii) of four bat species was significantly lower in farms undergoing the transitional period than in conventional farms, and P. kuhlii and H. savii were significantly less active in organic transitional farming systems that in organic-certified ones. Furthermore, the activity of the most dominant species (P. kuhlii) was significantly higher on organic than transitional and conventional citrus orchards, thus suggesting a time-lag effect. Landscape complexity measured as the amount of semi-natural areas did not moderate the effects of farming system for any study species.</li> <li> Synthesis and application. The transition to organic farming had persistent detrimental effects on bats and potentially on the pest suppression services they provide. Future agri-environmental policy should consider the transition period and implement measures to mitigate any negative effects on biodiversity, alongside promoting asynchronous transition of nearby farms. Our findings further highlight the crucial need to consider the time since transition to organic farming when assessing potential benefits of organic management on biodiversity.</li> </ol>