Integrating ecosystem engineering and food webs

Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non‐trophic interactions, we explore how we might best integrate ecosystem engineering and food webs. We provide rationales justifying their integration and present a provisional framework identifying how ecosystem engineering can affect the nodes and links of food webs and overall organization; how trophic interactions with the engineer can affect the engineering; and how feedbacks between engineering and trophic interactions can affect food web structure and dynamics. We use a simple integrative food chain model to illustrate how feedbacks between the engineer and the food web can alter 1) engineering effects on food web dynamics, and 2) food web responses to extrinsic environmental perturbations. We identify four general challenges to integration that we argue can readily be met, and call for studies that can achieve this integration and help pave the way to a more general understanding of interaction webs in nature. Synthesis All species are affected by their physical environment. Because ecosystem engineering species modify the physical environment and belong to food webs, such species are potentially one of the most important bridges between the trophic and non‐trophic. We examine how to integrate the so far, largely independent research areas of ecosystem engineering and food webs. We present a conceptual framework for understanding how engineering can affect food webs and vice versa, and how feedbacks between the two alter ecosystem dynamics. With appropriate empirical studies and models, integration is achievable, paving the way to a more general understanding of interaction webs in nature.     

Involvement of the Shewanella oneidensis decaheme cytochrome MtrA in the periplasmic stability of the beta-barrel protein MtrB

The Shewanella oneidensis outer membrane β-barrel protein MtrB is part of a membrane-spanning protein complex (MtrABC) which is necessary for dissimilatory iron reduction. Quantitative PCR, heterologous gene expression, and mutant studies indicated that MtrA is required for periplasmic stability of MtrB. DegP depletion compensated for this MtrA dependence.     

Temperature rather than photoperiod controls growth cessation and dormancy in Sorbus species

Environmental regulation of growth and dormancy of four Sorbus genotypes was studied in controlled environments. Emphasis was placed on assessment of the presence and nature of the deficient photoperiodic dormancy regulation system that has previously been reported for some woody Rosaceae species. Two genotypes of Sorbus aucuparia L. maintained indeterminate growth for 8 weeks and 9 weeks at temperatures of 15 °C and 21 °C in both 20 h and 10 h photoperiods, while at 9 °C, in the same photoperiodic conditions, they immediately ceased growing. At the higher temperatures, initiation of new leaves (nodes) was unaffected by photoperiod, while internode elongation was significantly enhanced by long days (LD). However, even after prolonged exposure to 9 °C, most plants resumed growth when moved to high temperature and LD, indicating a shallow state of dormancy. Seedlings of Sorbus intermedia (J. F. Ehrh.) Pers. and micro-propagated plantlets of S. commixta Hedl. 'Dodong' were also unaffected by photoperiod during primary growth, but failed to elongate and gradually became dormant regardless of temperature and day-length conditions. However, after chilling and breaking of dormancy, the plants elongated vigorously but changed to a determinate mode of growth. Furthermore, a temperature of 9 °C was found to be fully effective for breaking dormancy in S. intermedia plants. It is concluded that deficient photoperiodic dormancy control seems widespread in the Rosaceae and that, in such plants, both dormancy induction and release is brought about by low temperature. The potential impacts of climate change on such trees are discussed.     

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria

The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.     

Potential for bowhead whale entanglement in cod and crab pot gear in the Bering Sea

Bowhead whales (Balaena mysticetus) of the western Arctic stock winter in ice‐covered continental shelf regions of the Bering Sea, where pot fisheries for crabs (Paralithodes and Chionoecetes spp.) and Pacific cod (Gadus macrocephalus) pose a risk of entanglement. In the winter of 2008–2009 and 2009–2010 the spatial distribution of 21 satellite tagged bowhead whales partially overlapped areas in which pot fisheries for cod and blue king crab (Paralithodes platypus) occurred. However, these fisheries ended before whales entered the fishing areas, thus avoiding temporal overlap. A fishery for snow crab (Chionoecetes opilio) typically runs from January to May and provides the greatest potential for bowhead whales to encounter active pot gear. Tagged whales did not enter the area of the snow crab fishery during this study and generally remained in areas with >90% sea ice concentration, which is too concentrated for crab boats to penetrate. Pack ice sometimes overruns active fishing areas, resulting in lost gear, which is the most likely source of entanglement. The western Arctic stock of bowhead whales was increasing as of 2004; as such, incidental mortality from commercial pot fisheries is probably negligible at this time. Regardless, entanglement may increase over time and should be monitored.     

Ubiquitin-proteasome pathway modulates mouse oocyte meiotic maturation and fertilization via regulation of MAPK cascade and cyclin B1 degradation

Degradation of proteins mediated by ubiquitin-proteasome pathway (UPP) plays important roles in the regulation of eukaryotic cell cycle. In this study, the functional roles and regulatory mechanisms of UPP in mouse oocyte meiotic maturation, fertilization, and early embryonic cleavage were studied by drug-treatment, Western blot, antibody microinjection, and confocal microscopy. The meiotic resumption of both cumulus-enclosed oocytes and denuded oocytes was stimulated by two potent, reversible, and cell-permeable proteasome inhibitors, ALLN and MG-132. The metaphase I spindle assembly was prevented, and the distribution of ubiquitin, cyclin B1, and polo-like kinase 1 (Plk1) was also distorted. When UPP was inhibited, mitogen-activated protein kinase (MAPK)/p90rsk phosphorylation was not affected, but the cyclin B1 degradation that occurs during normal metaphase-anaphase transition was not observed. During oocyte activation, the emission of second polar body (PB2) and the pronuclear formation were inhibited by ALLN or MG-132. In oocytes microinjected with ubiquitin antibodies, PB2 emission and pronuclear formation were also inhibited after in vitro fertilization. The expression of cyclin B1 and the phosphorylation of MAPK/p90rsk could still be detected in ALLN or MG-132-treated oocytes even at 8 h after parthenogenetic activation or insemination, which may account for the inhibition of PB2 emission and pronuclear formation. We also for the first time investigated the subcellular localization of ubiquitin protein at different stages of oocyte and early embryo development. Ubiquitin protein was accumulated in the germinal vesicle (GV), the region between the separating homologous chromosomes, the midbody, the pronuclei, and the region between the separating sister chromatids. In conclusion, our results suggest that the UPP plays important roles in oocyte meiosis resumption, spindle assembly, polar body emission, and pronuclear formation, probably by regulating cyclin B1 degradation and MAPK/p90rsk phosphorylation.     

Polo-like kinase-1 is a pivotal regulator of microtubule assembly during mouse oocyte meiotic maturation,fertilization, and early embryonic mitosis

Polo-like kinases (Plks) are a family of serine/threonine protein kinases that have been activated through phosphorylation. The activity of these kinases has been shown to be required for regulating multiple stages of mitotic progression in somatic cells. In this experiment, the changes in Plk1 expression were detected in mouse oocytes through Western blotting. The subcellular localization of Plk1 during oocyte meiotic maturation, fertilization, and early cleavage as well as after antibody microinjection or microtubule assembly disturbance was studied by confocal microscopy. The quantity of Plk1 protein remained stable during meiotic maturation and decreased gradually after fertilization. Plk1 was localized to the spindle poles of both meiotic and mitotic spindles at the early M phase and then translocated to the middle region. At anaphase and telophase, Plk1 was concentrated at the midbody of cytoplasmic cleavages. Plk1 was concentrated between the male and female pronuclei after fertilization. Plk1 disappeared at the spindle region when microtubule formation was inhibited by colchicine or staurosporine, while it was concentrated as several dots in the cytoplasm after taxol treatment. Plk1 antibody injection decreased the germinal vesicle breakdown rate and distorted MI spindle organization. Our results indicate that Plk1 is a pivotal regulator of microtubule organization during mouse oocyte meiosis, fertilization, and cleavage and that its functions may be regulated by other kinases, such as staurosporine-sensitive kinases.     

Using Network Methodology to Infer Population Substructure

One of the main caveats of association studies is the possible affection by bias due to population stratification. Existing methods rely on model-based approaches like structure and ADMIXTURE or on principal component analysis like EIGENSTRAT. Here we provide a novel visualization technique and describe the problem of population substructure from a graph-theoretical point of view. We group the sequenced individuals into triads, which depict the relational structure, on the basis of a predefined pairwise similarity measure. We then merge the triads into a network and apply community detection algorithms in order to identify homogeneous subgroups or communities, which can further be incorporated as covariates into logistic regression. We apply our method to populations from different continents in the 1000 Genomes Project and evaluate the type 1 error based on the empirical p-values. The application to 1000 Genomes data suggests that the network approach provides a very fine resolution of the underlying ancestral population structure. Besides we show in simulations, that in the presence of discrete population structures, our developed approach maintains the type 1 error more precisely than existing approaches.