Determining the diet of larvae of the red rock lobster (Jasus edwardsii) using high-throughput DNA sequencing techniques

The diet of Jasus edwardsii during its ~2-year larval (phyllosoma) phase is largely unknown. High mortalities experienced during larviculture might be reduced if their diet were nutritionally modelled on the natural diet. Here, prey species were identified from phyllosoma midgut glands using 454 pyrosequencing of 18S rDNA. We found that gelatinous zooplankton, particularly Siphonophora and Ctenophora, occurred frequently in the midgut glands of phyllosomas, resolving previous conjecture that these animals are in the diet of J. edwardsii phyllosomas. A high occurrence of sequencing reads from unicellular microbes may also reflect a reliance on scavenging detritus.     

Design and use of group-specific primers and probes for real-time quantitative PCR

Real-time quantitative polymerase chain reaction (qPCR) has gained popularity as a technique to detect and quantify a specific group of target microorganisms from various environmental samples including soil, water, sediments, and sludge. Although qPCR is a very useful technique for nucleic acid quantification, accurately quantifying the target microbial group strongly depends on the quality of the primer and probe used. Many aspects of conducting qPCR assays have become increasingly routine and automated; however, one of the most important aspects, designing and selecting primer and probe sets, is often a somewhat arcane process. In many cases, failed or non-specific amplification can be attributed to improperly designed primer-probe sets. This paper is intended to provide guidelines and general principles for designing group-specific primers and probes for qPCR assays. We demonstrate the effectiveness of these guidelines by reviewing the use of qPCR to study anaerobic processes and biologic nutrient removal processes. qPCR assays using group-specific primers and probes designed with this method, have been used to successfully quantify 16S ribosomal Ribonucleic Acid (16S rRNA) gene copy numbers from target methanogenic and ammonia-oxidizing bacteria in various laboratory- and full-scale biologic processes. Researchers with a good command of primer and probe design can use qPCR as a valuable tool to study biodiversity and to develop more efficient control strategies for biologic processes.     

Physiological tolerance predicts species composition at different scales in a barnacle guild

This study examined how the species composition of an intertidal barnacle guild varied according to physical gradients in the environment at small scales governed by microclimates, medium scales of wave exposure and large scales of latitude. Barnacle distributions at small and medium scales were sampled in Ireland between 51°29′ and 52°44′N and 6°50′ and 10°08′W. Sampling on European shores spanned ~18° latitude from 37°05′ to 55°16′N. Barnacle surveys mainly took place in 2003–2004. An index of wave fetch was calculated along the wave exposure gradient using a digital coastline-based model that was supported by a biological exposure scale. A ‘dryness’ index was defined according to mean monthly wind speed, fetch along the average wind direction and mean monthly air or sea surface temperatures for 2 years (January 2001–December 2002) which is the period when the most recent adults in the barnacle community would have settled and grown to adulthood. The proportion of the dry-loving barnacle Chthamalus montagui Southward increased within the barnacle guild at all scales as the habitat became warmer and drier. Barnacle densities were high in all habitats, mean densities ranged from a minimum of 4.16 cm⁻² on moderately exposed shores to a maximum of 6.27 cm⁻² in sunlit or south-facing microclimates. Percentage cover of barnacles across the gradient of latitudes was usually >70%. The results suggest that the distribution and abundance of interacting barnacle species on European coasts is strongly controlled by abiotic factors, most likely temperature and desiccation.     

Worker drift and egg dumping by queens in wild Bombus terrestris colonies

Wild bumblebee colonies are hard to find and often inaccessible, so there have been few studies of the genetic structure of bumblebees within natural colonies, and hence, it is not clear how frequently events such as worker reproduction, worker drift and queen usurpation take place. This study aimed to quantify the occurrence of natal-worker reproduction, worker drift and drifter reproduction within 14 wild colonies of Bombus terrestris in Central Scotland. Four unlinked microsatellites were used to identify patterns of relatedness of the colonies’ adults and broods. In colonies with queens (queenright colonies), worker reproduction accounted for just 0.83 % of males, increasing to 12.11 % in queenless colonies. Four colonies contained a total of six workers which were not daughters of the queen, and were assumed to be drifters, and four male offspring of drifters. Drifting is clearly not common and results in few drifter offspring overall, although drifters produced approximately seven times more offspring per capita than workers that remained in their natal colony. Unexpectedly, two colonies contained clusters of sister workers and juvenile offspring that were not sisters to the rest of the adults or brood found in the colonies, demonstrating probable egg dumping by queens. A third colony contained a queen which was not a sister or daughter to the other bees in the colony. Although usurping of bumblebee colonies by queens in early season is well documented, this appears to be the first record of egg dumping, and it remains unclear whether it is being carried out by old queens or newly mated young queens.     

How age and sex drive the foraging behaviour in the king penguin

As predicted by life history theory, once recruited into the breeding population and with increasing age, long-lived animals should be able to manage more efficiently the conflict between self-maintenance and reproduction. Consequently, breeding performances should improve with age before stabilizing at a certain level. Using temperature–depth recorders and isotopic analysis, we tested how age affects the foraging behaviour of king penguin Aptenodytes patagonicus during one trip in the chick-rearing phase. Depending on sex and age, king penguins expressed two different foraging strategies. Older birds gained more daily mass per unit body mass than younger ones. Older females conducted shorter trips, dived deeper and performed more prey pursuits. They also had higher blood levels of δ¹⁵N than younger individuals and males indicating sex- and age-specific dietary regimes. However, we found no differences in carbon isotopic signature, suggesting that individuals exploited the same foraging areas independently of sex and age. Our results suggest that king penguins are able to increase the quantity of energy extracted with increasing age and that such a strategy is sex-related. Our study is the first to reveal of an interaction between age and sex in determining foraging efficiency in king penguins.     

Microhabitat association in white-streaked grouper Epinephelus ongus: importance of Acropora spp.

Microhabitat associations are considered to be important for juvenile survivorship and growth of coral reef fishes. The aim of the study was to quantify microhabitat associations between juvenile and adult white-streaked grouper Epinephelus ongus, which supports important fisheries in coral reef areas. Underwater observations revealed that most juveniles were found in bottlebrush Acropora spp., staghorn Acropora spp. and coral rubble and there was a significant positive use of bottlebrush Acropora spp. and a significant negative use of coral rubble. For adults, most individuals were found in bottlebrush Acropora spp. and staghorn Acropora spp., and there was a significant positive use of staghorn Acropora spp. and significant negative use of coral rubble. A habitat choice experiment by using pre-settlement individuals revealed that both bottlebrush Acropora spp. and staghorn Acropora spp. were used as settlement sites, whereas coral rubble was rarely used as a settlement site. Results of the study suggest that juvenile and adult E. ongus showed significantly positive microhabitat associations with bottlebrush Acropora spp. and staghorn Acropora spp., respectively, in the field. Bottlebrush Acropora spp. has smaller inter-branch spaces than staghorn Acropora spp., which could drive patterns of microhabitat associations. In addition, post-settlement processes such as predation may influence the spatial distribution of juveniles. Because Acropora corals are very susceptible to coral bleaching, we predict that rising temperatures from climate change will negatively impact populations of E. ongus.     

Detection of polychlorinated biphenyls employing chemical dechlorination followed by biphenyl whole cell sensing system

Polychlorinated biphenyls (PCBs) are a mixture of 209 individual chlorinated compounds commonly known as PCB congeners. These compounds are hydrophobic and are persistent in the environment. Their use was banned in the US a few decades ago because of harmful health effects. Therefore, detection of PCBs in environmental samples is increasingly important. To that end, we have developed a two-step simple and sensitive method for the detection of total PCBs. Specifically, our method involves dechlorination of PCBs to biphenyl followed by detection of biphenyl using a whole cell sensing system as the detection system. The whole cell sensing system consists of cells of the strain Pseudomonas pseudoalcaligenes KF707 harboring plasmid pSD7000. Plasmid pSD7000 contains the gene of lacZ, a reporter protein under the control of the bph operon. The detection is achieved through the emission of light afforded by the expression of reporter protein triggered by the presence of biphenyl. Due to the fact that this operon is activated only by few PCB congeners, a chemical dechlorination method was employed to convert all PCBs to biphenyl, and thus all the PCBs present in a given sample are able to be detected. The results showed that PCB congeners were rapidly (30?min) and efficiently (>98.5%) dechlorinated to biphenyl using a Mg/K₂PdCl₆ catalyst, and the biphenyl could be subsequently quantified using the whole cell sensing system. This hybrid analytical method that combines classical dechlorination with novel biosensing methods may find applications in the on-site monitoring of PCBs contamination levels.     

NGOs come and go but business continues: lessons from co-management institutional arrangements for governance of the Arabuko-Sokoke Forest Reserve in Kenya

The objective of this paper is to examine the current institutional arrangements for governance of the Arabuko-Sokoke Forest Reserve (ASFR) and show their major contribution in the ASFR co-management business of conserving the forest and providing livelihoods to the poor forest-dependent communities. Despite the fact that funding from non-governmental organizations ended, the ASFR co-management business did not stall. The institutional arrangements for co-management were deemed to be the major component that contributed to the continuation of the ASFR co-management business. To demonstrate this hypothesis, the paper explores four main areas that shape the institutional arrangement of the ASFR co-management regime, informed by common property theories: (1) how governance arrangement structures for the ASFR are organized; (2) villagers’ perceptions and awareness of the co-management structure; (3) co-management arrangement for access, ownership and use of the various forest resources; and (4) importance of the forest resources to the households. The co-management piloting and non-piloting communities adjacent to the forest and who have been depending on the forest as a source of their livelihoods are compared in order to understand the role of the ASFR co-management institutional arrangements in the sustainability of its business.