Partitioning of soil CO2 flux components in a temperate grassland ecosystem

We deployed an automated multiplexed soil‐respiration (SR) system to monitor partitioned soil CO₂ component fluxes (from roots, mycorrhizal hyphae and heterotrophs) in a UK grassland using a combination of shallow surface (total SR flux), deep (excluding roots and mycorrhizal fungi) and 20‐µm pore mesh window soil collars (excluding roots only). Soil CO₂ efflux was monitored during a 3‐month period during summer. Repeated cutting of mycorrhizal connections in some of the mycorrhizal treatments enabled assessment of subsequent recovery of mycorrhizal fluxes and a comparison with deep collar fluxes. After soil collar insertion, fluxes in the deep collars were significantly reduced, by approximately 40%. Whereas fluxes in the uncut, mycorrhizal collar treatments remained close to those from the surface collar, cut mycorrhizal treatments showed an immediate reduction after cutting to values close to those from the deep collar with a subsequent recovery of around 4 weeks. Overall, the autotrophic root and mycorrhizal flux was relatively stable throughout. Whereas root fluxes contributed about 10–30% of the total flux during the initial larger flux period, this declined and there was an increased mycorrhizal contribution during the latter part of the measurement period. Moreover, SR flux components differed in their response to key climatic factors, with root fluxes responding equally to temperature and light. Importantly, whereas the heterotrophic flux component responded strongly to temperature and soil moisture, the mycorrhizal component responded much less to those factors, but more to light. We also investigated treatment impacts over time on soil biochemical variables such as microbial biomass C, extractable C, microbial quotient and metabolic quotient, and bacterial community structure, and discussed these in relation to measured SR fluxes and the partitioning technique.     

Genetic diversity and species identification of Argulus parasites collected from major aquaculture regions of India using RAPD‐PCR

Argulus is one of the most important fish parasites that cause heavy economic loss to aquaculture industry. The present investigation was undertaken to study the genetic diversity of the Argulus sp. collected from 13 locations representing major aquaculture zones in India by RAPD analysis and to develop species‐specific markers. Thirteen random decamer primers were used to amplify DNA fragments from three individual parasites of each location. Of the 172 bands scored by the primers, 168 were polymorphic. The per cent polymorphic loci and gene diversity values varied within a range of 8.14–43.02 and 0.0342–0.1727 respectively. Nei's genetic similarity between populations across all the primers ranged from 0.363 to 0.969. The dendrogram based on Nei's genetic distance showed two clusters; Bangalore and Mandi populations forming one cluster, and the rest in another cluster. The clusters also revealed strong correlation with the species identified as A. japonicus and A. siamensis respectively by morphological method. The study thus indicated A. siamensis as the major prevalent species in carp culture farms in India. Species‐specific primers were designed from unique sequences cloned from RAPD fragments that could able to identify A. siamensis and A. japonicus separately.     

Effects of cage fish farming on phytoplankton community structure,biomass and primary production in an aquaculture area in the middle Adriatic Sea

In this study, we investigated the physical, chemical and biological parameters of the water column at two stations under different trophic conditions during a 1‐year period (from September 2005 to September 2006) in an aquaculture area. The investigation was performed monthly at a station inside the fish farm in Maslinova Bay (middle Adriatic Sea, Croatia) and at a control station located in the Hvar Channel in the vicinity of the farm. The results showed that the concentrations of dissolved nutrients were slightly enhanced at the farm station in comparison with the control station, although those differences were not statistically significant, nor were the differences in oxygen saturation recorded during the investigation period. As opposed to the chemical parameters, considerably higher deviations were recorded for biological parameters as demonstrated by a significant increase in phytoplankton biomass and primary production (measured in situ) at the farm station, particularly during the summer season. Phytoplankton community structure analysis showed that the phytoplankton composition at the farm was mostly determined by seasonal changes rather than by the influence of fish farming. In Maslinova Bay, no causal links were identified between increased biomass and the appearance of toxic species.     

Fish condition as an indicator of stock status: Insights from condition index in a food-limiting environment

Individual performance defines population dynamics. Condition index – a ratio of weight and some function of length – has been louded as an indicator of individual performance and recommended as a tool in fisheries management and conservation. However, insufficient understanding of the correlation between individual-level processes and population-level responses hinders its adoption. To this end, we use composite modelling to link individual's condition, expressed through the condition index, to population-level status. We start by modelling ontogeny of European pilchard (Sardina pilchardus, Clupeidae) as a function of food and constant temperature using Dynamic Energy Budget theory. We then provide a framework to simultaneously track the individual- and population-level statistics by incorporating the dynamic energy budget model into an individual-based model. Lastly, we explore the effects of fishing pressure on the statistics in two constant and food-limited environmental carrying capacity scenarios. Results show that, regardless of the species' environmental carrying capacity, individual condition index will increase with fishing mortality, that is, with reduction of stock size. Same patterns are observed for gilthead seabream (Sparus aurata, Sparidae), a significantly different species. Condition index can, therefore, in food-limited populations, be used to (i) estimate population size relative to carrying capacity and (ii) distinguish overfished from underfished populations. Our findings promote a practical way to operationally incorporate the condition index into fisheries management and marine conservation, thus providing additional use for the commonly collected biometric data. Some real-world applications, however, may require additional research to account for other variables such as fluctuating environmental conditions and individual variability.     

Effects of fish farming on microbial planktonic communities in the middle Adriatic sea

The effects of farming on planktonic microbial communities were investigated at the coastal sea bass/sea bream farm in the oligotrophic middle Adriatic Sea. Analyses of nutrients, chlorophyll a, cyanobacteria (Prochlorococcus), heterotrophic bacteria and nanoflagellates (both pigmented and heterotrophic) were carried out on samples taken during six seasonal cruises at different water depths. Farming activity increased the natural concentrations of some nutrients (ammonium, nitrite, phosphate, dissolved inorganic nitrogen) and changed their seasonal pattern. The values still remained typical for oligotrophic environ‐ments demonstrating no risk for eutrophication. Enhanced nutrient supply provoked an immediate increase in abundances of both autotrophic and heterotrophic microbial groups (except pigmented nanoflagellates) and chlorophyll a. The effect of farming was more visible for the heterotrophic microbial component. Results from this study reveal a potential common pattern of microbial response to farming in the oligotrophic environments. It also suggests the importance of heterotrophic microbial web in transferring the matter and energy released from the fish farms in nutrient poor environments.     

Phylogenetic analysis of intestinal bacteria of freshwater salmon Salmo salar and sea trout Salmo trutta trutta and diet

The microbial diversity of culturable intestinal microflora of wild freshwater salmonid fishes salmon Salmo salar and sea trout Salmo trutta trutta juveniles (0+ years old) from the same environmental conditions were investigated by means of molecular identification techniques and analysis of diet. Significant differences in the intestinal microbial diversity were observed in different fish species. The predominant group in the intestinal tract of the salmon comprised representatives of the Enterobacteriaceae family (23%), Plesiomonas (19.2%) and Carnobacterium (15.3%). Predominant microbiota in sea trout intestinal tract were Enterobacteriaceae (52%), Aeromonas (22%) and Pseudomonas (14%). The results show that Enterobacteriaceae were predominant in the intestinal tract of the salmon and the sea trout juveniles raised on diets of different compositions. However, molecular identification of the intestinal microbiota at the species or genus level revealed differences in these fish species. Bacteria in the hindgut of salmon included Pragia and Serratia. However, bacteria in the gut contents of sea trout from the Enterobacteriaceae family were Buttiauxella, Enterobacter, Moellerella, Pantoea, Rahnella and Tiedjeia arctica. A novel phylotype of T. arctica is harbored in the intestinal tract of wild salmon, and may correspond to a previously undescribed species.     

Feeding behaviour of green mussels,Perna viridis farmed in Marudu Bay,Malaysia

The green mussel, Perna viridis is known to have the ability to selectively ingest certain suspended particles from water. However, the preferential ingestion of specific phytoplankton taxa by P. viridis under different environmental conditions is not well understood. A study was undertaken to identify the phytoplankton taxa that are preferentially ingested and rejected by P. viridis in different environmental conditions at Marudu Bay, Malaysia. Phytoplankton abundance and composition in stomach and surrounding waters were determined microscopically. The gonad development stages of P. viridis and various environmental parameters of the bay including temperature, salinity, dissolved oxygen, current speed, pH, visibility, chlorophyll a, nutrients concentration and suspended particles were also determined. Results of current study demonstrated that selective ingestion in P. viridis was mainly influenced by seston concentration, phytoplankton abundance and composition. At high seston concentration with low phytoplankton abundance, P. viridis selectively ingested Coscinodiscus spp. In contrast, P. viridis was found to ingest wider range of phytoplankton at low seston concentration and high phytoplankton abundance. Interestingly, Chaetoceros spp. and Bacteriastrum spp. were selectively rejected by P. viridis in both high and low seston conditions. Nevertheless, no selective ingestion behaviour was evidenced in low seston with low phytoplankton conditions. Besides phytoplankton, zooplankton has also contributed significantly in the diet of P. viridis, where high numbers of copepod and bivalve larvae were found in the stomach. The findings of current study can be useful in determining potential farming sites for green mussel in future.     

Mycobacteria in aquarium fish: results of a 3‐year survey indicate caution required in handling pet‐shop fish

Fish are commonly infected with non‐tuberculous mycobacteria (NTM), which should be regarded as potential pathogens when handling aquarium fish and equipment. This study examined 107 aquarium fish from pet shops. Cultivation of the fish samples using different selective media was conducted for identification of NTM. Isolates were identified using the GenoType Mycobacterium common mycobacteria and additional species assays, sequencing of the 16S rRNA and rpoB genes, and real‐time PCR assay for identification of Mycobacterium (M.) marinum. Among the investigated fish, 79.4% (85/107) were positive for mycobacteria, with 8.2% (7 of 85) having two mycobacterial species present. Among the positive fish, the common pathogens M. marinum, Mycobacterium fortuitum (M. fortuitum group) and Mycobacterium chelonae were identified in approx. 90% of fish and other NTM species in 10%, including Mycobacterium peregrinum/septicum, Mycobacterium gordonae, Mycobacterium arupense, Mycobacterium kansasii, Mycobacterium ulcerans and Mycobacterium setense. The well‐known human pathogen M. marinum was present in 10.6% of the positive fish (9 of 85). The species of mycobacteria identified in the study are not only recognized as aquarium fish pathogens, but can also cause pathology in humans. Microbiological and clinical communities should therefore be sensitized to the role of NTM in infections associated with exposure to aquarium fish.     

Protease in sturgeon sperm and the effects of protease inhibitors on sperm motility and velocity

In mammals, proteases are present in sperm acrosome and play key role in fertilization. Sturgeon sperm has an acrosome, but its physiology, biochemistry, and potential role in fertilization are unknown. In the present study, we have observed high protease activity in acidic extract of intact sperm compared to that of seminal plasma in sterlet (Acipenser ruthenus). The protease activity was decreased and increased in acidic extract of motility-activated sperm and in the activation medium, respectively. Molecular analysis revealed total protease and serine (acrosin) protease activities in sperm acidic extract which was accumulated in a protein band with relative molecular mass of 35 kDa. Immunoelectron microscopy using an affinity-purified polyclonal antibody for boar acrosin localized the protease at the acrosome region. Moreover, initiation of sperm motility was inhibited after activation in the presence of inhibitors for both trypsin-like and chymotrypsin-like proteases, while the effects of protease inhibitors on sperm velocity were uncertain. Our results indicate similarities in physiology and biochemistry of acrosome between sturgeon and mammals and suggest potential role of protease in the initiation of sperm motility in sturgeon.     

Quantifying differences in total tract nutrient digestibilities between goats and sheep

Conclusions from narrative qualitative reviews on differences in total tract digestibilities between goats and sheep did not account for variability among studies. Therefore meta‐analytic techniques were used to describe the magnitude of these differences with numerical values. A unitless effect size (Hedges’ g) was applied within studies to measure differences in digestibilities of dry matter (DM; 104 comparisons), organic matter (OM; 93 comparisons), crude protein (CP; 85 comparisons), neutral detergent fibre (NDF; 74 comparisons), acid detergent fibre (ADF; 59 comparisons), cellulose (24 comparisons), hemicellulose (18 comparisons) and gross energy (GE; 29 comparisons). The absence and inability to describe independent factors which contributed to variation among studies necessitated the use of frequentist random effects and hierarchical Bayesian models in the calculation of summary statistics across studies. Digestibilities of DM, OM, CP, NDF, ADF and hemicellulose were higher (p < 0.05) in goats than sheep when all‐forage diets were fed. When concentrates were included in the diets, there were no such differences. Differences between goats and sheep in DM intake were found to be non‐significant. Differences in nutrient digestibilities of forages as sole feed implies that species‐specific values have to be used in feed formulation and feeding strategies. However, caution is needed when extrapolating results from stall‐feeding, which is how digestibility data are usually measured, to grazing conditions.