Multi-species occurrence models to evaluate the effects of conservation and management actions

Conservation and management actions often have direct and indirect effects on a wide range of species. As such, it is important to evaluate the impacts that such actions may have on both target and non-target species within a region. Understanding how species richness and composition differ as a result of management treatments can help determine potential ecological consequences. Yet it is difficult to estimate richness because traditional sampling approaches detect species at variable rates and some species are never observed. We present a framework for assessing management actions on biodiversity using a multi-species hierarchical model that estimates individual species occurrences, while accounting for imperfect detection of species. Our model incorporates species-specific responses to management treatments and local vegetation characteristics and a hierarchical component that links species at a community-level. This allows for comprehensive inferences on the whole community or on assemblages of interest. Compared to traditional species models, occurrence estimates are improved for all species, even for those that are rarely observed, resulting in more precise estimates of species richness (including species that were unobserved during sampling). We demonstrate the utility of this approach for conservation through an analysis comparing bird communities in two geographically similar study areas: one in which white-tailed deer (Odocoileus virginianus) densities have been regulated through hunting and one in which deer densities have gone unregulated. Although our results indicate that species and assemblage richness were similar in the two study areas, point-level richness was significantly influenced by local vegetation characteristics, a result that would have been underestimated had we not accounted for variability in species detection.     

The role of floods and droughts on riverine ecosystems under a changing climate

Floods and droughts are key driving forces shaping aquatic ecosystems. Climate change may alter key attributes of these events and consequently health and distribution of aquatic species. Improved knowledge of biological responses to different types of floods and droughts in rivers should allow the better prediction of the ecological consequences of climate change‐induced flow alterations. This review highlights that in unmodified ecosystems, the intensity and direction of biological impacts of floods and droughts vary, but the overall consequence is an increase in biological diversity and ecosystem health. To predict the impact of climate change, metrics that allow the quantitative linking of physical disturbance attributes to the directions and intensities of biological impacts are needed. The link between habitat change and the character of biological response is provided by the frequency of occurrence of the river wave characteristic—that is the event's predictability. The severity of impacts of floods is largely related to the river wave amplitude (flood magnitude), while the impact of droughts is related to river wavelength (drought duration).     

Investigating the in situ degradation of atrazine in groundwater

This study focused on whether or not atrazine could be degraded by indigenous groundwater bacteria as part of an in situ remediation approach. Groundwater was taken from an unconfined middle upper chalk site where concentrations of atrazine and nitrate were typically in the ranges 0.02-0.2 microg litre-1 and 11.6-25.1 mg NO3-N litre-1 respectively. Sacrificial batch studies were performed using this groundwater spiked with atrazine at a concentration of 10 microg litre-1 in conjunction with a minimal mineral salts liquid (Glu-MMSL) medium which contained glucose as the sole carbon source. Treatments comprised either the Glu-MMSL groundwater cultured bacteria or Pseudomonas sp. strain ADP. Results from sacrificial batches indicated the occurrence of bacterial growth and denitrification as monitored by optical density (absorbance at 600 nm) and NO3-N content. Analysis of atrazine content by solid phase extraction coupled with high-performance liquid chromatography showed no degradation of atrazine over a period of 103 days in either treatment. These results indicated that no acclimatised bacterial community featuring positive degraders to the herbicide atrazine had become established within this chalk aquifer in response to the trace levels encountered.     

The Norwegian Healthier Goats programme – A financial cost–benefit analysis

The aim of this study was to evaluate the profitability to dairy goat farmers of participating in the Healthier Goats disease control and eradication programme (HG), which was initiated in 2001 and is still running. HG includes the control and eradication of caprine arthritis encephalitis (CAE), caseous lymphadenitis (CLA) and paratuberculosis (Johne's disease) in Norwegian goat herds.     

Coastal ecosystem-based management with nonlinear ecological functions and values

A common assumption is that ecosystem services respond linearly to changes in habitat size. This assumption leads frequently to an "all or none" choice of either preserving coastal habitats or converting them to human use. However, our survey of wave attenuation data from field studies of mangroves, salt marshes, seagrass beds, nearshore coral reefs, and sand dunes reveals that these relationships are rarely linear. By incorporating nonlinear wave attenuation in estimating coastal protection values of mangroves in Thailand, we show that the optimal land use option may instead be the integration of development and conservation consistent with ecosystem-based management goals. This result suggests that reconciling competing demands on coastal habitats should not always result in stark preservation-versus-conversion choices.     

Seasonal Surface Drainage of Sloping Farmland: A Review of Its Hydrogeomorphic Impacts

The combination of runoff‐generating areas (saturated soils) and overland flow concentration in features such as drainage ditches makes sloping farmland vulnerable to soil erosion. The establishment of drainage ditches aims at draining the excess of water from the farmland, particularly in areas where soils are saturated in the rainy season. The hydrogeomorphic impacts on the farmland itself and on downstream areas need however also to be studied. Off site, downstream problems comprise higher peak discharges, leading to gully initiation, an increase in sediment load, and flooding problems. On‐site problems such as the development of the drainage ditches into (ephemeral) gullies are less documented, although they may be important, as illustrated in the Lake Tana Basin (Ethiopia). The similarities and interactions between ephemeral gully channels and drainage ditches have to be considered to better understand all effects of drainage. Drainage ditches are a potential source of conflict between farmers with different interests and power, as well as between upstream and downstream users. A case study on drainage ditches on sloping farmlands in the Lake Tana Basin showed that nine out of ten catchments had drainage densities by ditches ranging from 53 to 510 m ha⁻¹. Drainage ditches were constructed with an average top width of 27 (±9) cm. A significant correlation was found between stone bund density (physical conservation structures) and ditch drainage density (R = −0·72), in line with the Ethiopian government's ban on drainage ditches in farmlands where stone bunds have been constructed. Copyright © 2014 John Wiley & Sons, Ltd.     

Intramammary antibiotics with complementary acupuncture decreases milk serum N-acetyl-beta-D-glucosaminidase concentrations in dairy cattle with subclinical mastitis

The objective of this research is to determine whether intramammary antibiotics with complementary acupuncture can reduce bovine mammary inflammation due to subclinical mastitis. Lactating cows were selected based on milk with a somatic cell count (SCC) greater than 500,000 cells/ml. Pre- and post-treatment milk samples were collected to determine SCC, aerobic bacterial content, milk ion conductivity, total protein, lactate dehydrogenase (LDH) and N-acetyl-beta-D-glucosaminidase (NAGase) concentrations. Milk serum was prepared from milk samples by double centrifugation. Concentrations of LDH and NAGase were determined using commercial enzyme-linked immunosorbent assays. Cows being treated with intramammary antibiotics were separated by random assignment to the acupuncture group (n = 10) and a no-acupuncture (control) group (n = 9). Both the acupuncture and control group were restrained for 30 min in a head catch 12 hr apart for a total of four times. For front quarters affected by subclinical mastitis, the acupuncture points used were spleen (SP) 12, SP 17, SP 18, SP 21, stomach (ST) 18 and conception vessel (CV) 12. For rear quarters affected by subclinical mastitis, the acupuncture points used were bladder (BL) 30, BL 30-1, BL 49, kidney (KI) 10, conception vessel (CV) 2 and CV 3. All parameters were compared using a Student t test. Significance was defined as p < .05. Compared to control cows, complementary acupuncture treatment reduced NAGase enzymatic activity in quarters of cows with subclinical mastitis. The reduction in NAGase suggests that complementary acupuncture treatment may be associated with healing of the damaged mammary epithelial cells, which are the primary source of NAGase activity in milk serum.     

Improving the detection of rare native fish species in environmental DNA metabarcoding surveys

1. The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. In New South Wales, these decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species.
2. Although the use of environmental DNA (eDNA) monitoring, in particular eDNA metabarcoding, achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers.
3. A laboratory and field-based pilot study was used to address this knowledge gap and assess the impact of a blocking primer, targeting cyprinid fishes (including carp), on the detection probabilities of native species and the minimum sampling effort required.
4. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.