Diversity of condensed tannin structures affects rumen in vitro methane production in sainfoin (Onobrychis viciifolia) accessions

Sainfoin is a non-bloating temperate forage legume with a moderate-to-high condensed tannin (CT) content. This study investigated whether the diversity of sainfoin accessions in terms of CT structures and contents could be related to rumen in vitro gas and methane (CH4) production and fermentation characteristics. The aim was to identify promising accessions for future investigations. Accessions differed (P < 0·0001) in terms of total gas and CH4 productions. Fermentation kinetics (i.e. parameters describing the shape of the gas production curve and half-time gas production) for CH4 production were influenced by accession (P ≤ 0·038), but not by PEG. Accession, PEG and time affected (P < 0·001) CH4 production, but accession and PEG interaction showed only a tendency (P = 0·08). Increase in CH4 due to PEG addition was not related to CT content. Further analysis of the relationships among multiple traits (nutritional composition, CT structure and CH4 production) using principal component analysis (PCA) based on optimally weighted variables revealed differences among accessions. The first two principal component axes, PC1 (57·6%) and PC2 (18·4%), explained 76·0% of the total variation among accessions. Loading of biplots derived from both PCAs made it possible to establish a relationship between the ratio of prodelphinidin:procyanidin (PD:PC) tannins and CH4 production in some accessions. The PD:PC ratio seems to be an important source of variation that is negatively related to CH4 production. These results suggested that sainfoin accessions collected from across the world exhibited substantial variation in terms of their effects on rumen in vitro CH4 production, revealing some promising accessions for future investigations.

The inclusion of forage mixtures in the diet of growing dairy heifers: impacts on digestion, energy utilisation, and methane emissions

Intensive farming focusing on monoculture grass species to maximise forage production has led to a reduction in the extent and diversity of species-rich grasslands. However, plant communities with higher species number (richness) are a potential strategy for more sustainable production and mitigation of greenhouse gas (GHG) emissions. Research has indicated the need to understand opportunities that forage mixtures can offer sustainable ruminant production systems. The objective of the two experiments reported here were to evaluate multiple species forage mixtures in comparison to ryegrass-dominant pasture, when conserved or grazed, on digestion, energy utilisation, N excretion, and methane emissions by growing 10–15 month old heifers. Experiment 1 was a 4 × 4 Latin square design with five week periods. Four forage treatments of: (1) ryegrass (control); permanent pasture with perennial ryegrass (Lolium perenne); (2) clover; a ryegrass:red clover (Trifolium pratense) mixture; (3) trefoil; a ryegrass:birdsfoot trefoil (Lotus corniculatus) mixture; and (4) flowers; a ryegrass:wild flower mixture of predominately sorrel (Rumex acetosa), ox-eye daisy (Leucanthemum vulgare), yarrow (Achillea millefolium), knapweed (Centaurea nigra) and ribwort plantain (Plantago lanceolata), were fed as haylages to four dairy heifers. Measurements included digestibility, N excretion, and energy utilisation (including methane emissions measured in respiration chambers). Experiment 2 used 12 different dairy heifers grazing three of the same forage treatments used to make haylage in experiment 1 (ryegrass, clover and flowers) and methane emissions were estimated using the sulphur hexafluoride (SF6) tracer technique. Distribution of ryegrass to other species (dry matter (DM) basis) was approximately 70:30 (clover), 80:20 (trefoil), and 40:60 (flowers) for experiment 1. During the first and second grazing rotations (respectively) in experiment 2, perennial ryegrass accounted for 95 and 98% of DM in ryegrass, and 84 and 52% of DM in clover, with red clover accounting for almost all of the remainder. In the flowers mixture, perennial ryegrass was 52% of the DM in the first grazing rotation and only 30% in the second, with a variety of other flower species occupying the remainder. Across both experiments, compared to the forage mixtures (clover, trefoil and flowers), ryegrass had a higher crude protein (CP) content (P < 0.001, 187 vs. 115 g kg −1 DM) and DM intake (P < 0.05, 9.0 vs. 8.1 kg day −1). Heifers in experiment 1 fed ryegrass, compared to the forage mixtures, had greater total tract digestibility (g kg −1) of DM (DMD; P < 0.008, 713 vs. 641) and CP (CPD, P < 0.001, 699 vs. 475), and used more intake energy (%) for body tissue deposition (P < 0.05, 2.6 vs. −4.9). For both experiments, heifers fed flowers differed the most compared to the ryegrass control for a number of measurements. Compared to ryegrass, flowers had 40% lower CP content (P < 0.001, 113 vs. 187 g kg −1), 18% lower DMD (P < 0.01, 585 vs. 713 g kg −1), 42% lower CPD (P < 0.001, 407 vs. 699 g kg −1), and 10% lower methane yield (P < 0.05, 22.6 vs. 25.1 g kg −1 DM intake). This study has shown inclusion of flowers in forage mixtures resulted in a lower CP concentration, digestibility and intake. These differences were due in part to sward management and maturity at harvest. Further research is needed to determine how best to exploit the potential environmental benefits of forage mixtures in sustainable ruminant production systems.

Only connect: an annotated bibliography reflecting the breadth and diversity of systems thinking

The field of systems thinking is both broad and diverse. This paper tries to provide assistance to outsiders wishing to find out what systems thinking is and also to insiders interested in exploring areas of the systems movement other than their own. A selection of books, papers and articles is given. Each has a full reference and a brief annotation, this being an account of, and a critical comment on, its content. The selection does not aim to be definitive or authoritative and obviously displays the predilections of the authors. However, the hope is that it will convey a sense of the intellectual and practical endeavours that, to the authors, constitute systems thinking and that it may aid the exploration of the range of holistic ideas that people have found useful in thinking about and acting in the world.

Pollinator conservation: the difference between managing for pollination services and preserving pollinator diversity

Our review looks at pollinator conservation and highlights the differences in approach between managing for pollination services and preserving pollinator diversity. We argue that ecosystem service management does not equal biodiversity conservation, and that maintaining species diversity is crucial in providing ecosystem resilience in the face of future environmental change. Management and policy measures therefore need to focus on species not just in human dominated landscapes but need to benefit wider diversity of species including those in specialised habitats. We argue that only by adopting a holistic ecosystem approach we can ensure the conservation and sustainable use of biodiversity and ecosystem services in the long-term.

The impact of westerly wind bursts and ocean initial state on the development, and diversity of El Niño events

Westerly wind bursts (WWBs) that occur in the western tropical Pacific are believed to play an important role in the development of El Niño events. Here, following the study of Lengaigne et al. (Clim Dyn 23(6):601–620, 2004), we conduct numerical simulations in which we reexamine the response of the climate system to an observed wind burst added to a coupled general circulation model. Two sets of twin ensemble experiments are conducted (each set has control and perturbed experiments). In the first set, the initial ocean heat content of the system is higher than the model climatology (recharged), while in the second set it is nearly normal (neutral). For the recharged state, in the absence of WWBs, a moderate El Niño with a maximum warming in the central Pacific (CP) develops in about a year. In contrast, for the neutral state, there develops a weak La Niña. However, when the WWB is imposed, the situation dramatically changes: the recharged state slides into an El Niño with a maximum warming in the eastern Pacific, while the neutral set produces a weak CP El Niño instead of previous La Niña conditions. The different response of the system to the exact same perturbations is controlled by the initial state of the ocean and the subsequent ocean–atmosphere interactions involving the interplay between the eastward shift of the warm pool and the warming of the eastern equatorial Pacific. Consequently, the observed diversity of El Niño, including the occurrence of extreme events, may depend on stochastic atmospheric processes, modulating El Niño properties within a broad continuum.

Diversity of STs, plasmids and ESBL genes among Escherichia coli from humans, animals and food in Germany, the Netherlands and the UK

This study aimed to compare ESBL-producing Escherichia coli causing infections in humans with infecting or commensal isolates from animals and isolates from food of animal origin in terms of the strain types, the ESBL gene present and the plasmids that carry the respective ESBL genes. A collection of 353 ESBL-positive E. coli isolates from the UK, the Netherlands and Germany were studied by MLST and ESBL genes were identified. Characterization of ESBL gene-carrying plasmids was performed using PCR-based replicon typing. Moreover, IncI1-Iγ and IncN plasmids were characterized by plasmid MLST. The ESBL-producing E. coli represented 158 different STs with ST131, ST10 and ST88 being the most common. Overall, blaCTX-M-1 was the most frequently detected ESBL gene, followed by blaCTX-M-15, which was the most common ESBL gene in the human isolates. The most common plasmid replicon type overall was IncI1-Iγ followed by multiple IncF replicons. ESBL genes were present in a wide variety of E. coli STs. IncI1-Iγ plasmids that carried the blaCTX-M-1 gene were widely disseminated amongst STs in isolates from animals and humans, whereas other plasmids and STs appeared to be more restricted to isolates from specific hosts.

The effectiveness of protected areas in the conservation of species with changing geographical ranges

A cornerstone of conservation is the designation and management of protected areas (PAs): locations often under conservation management containing species of conservation concern, where some development and other detrimental influences are prevented or mitigated. However, the value of PAs for conserving biodiversity in the long term has been questioned given that species are changing their distributions in response to climatic change. There is a concern that PAs may become climatically unsuitable for those species that they were designated to protect, and may not be located appropriately to receive newly-colonizing species for which the climate is improving. In the present study, we analyze fine-scale distribution data from detailed resurveys of seven butterfly and 11 bird species in Great Britain aiming to examine any effect of PA designation in preventing extinctions and promoting colonizations. We found a positive effect of PA designation on species' persistence at trailing-edge warm range margins, although with a decreased magnitude at higher latitudes and altitudes. In addition, colonizations by range expanding species were more likely to occur on PAs even after altitude and latitude were taken into account. PAs will therefore remain an important strategy for conservation. The potential for PA management to mitigate the effects of climatic change for retracting species deserves further investigation.

Effects of species turnover on reserve site selection in a fragmented landscape

Changes in species composition is an important process in many ecosystems but rarely considered in systematic reserve site selection. To test the influence of temporal variability in species composition on the establishment of a reserve network, we compared network configurations based on species data of small mammals and frogs sampled during two consecutive years in a fragmented Atlantic Forest landscape (SE Brazil). Site selection with simulated annealing was carried out with the datasets of each single year and after merging the datasets of both years. Site selection resulted in remarkably divergent network configurations. Differences are reflected in both the identity of the selected fragments and in the amount of flexibility and irreplaceability in network configuration. Networks selected when data for both years were merged did not include all sites that were irreplaceable in one of the 2 years. Results of species number estimation revealed that significant changes in the composition of the species community occurred. Hence, temporal variability of community composition should be routinely tested and considered in systematic reserve site selection in dynamic systems.

A comparative study of cleaning activity of two reef fishes at Fernando de Noronha Archipelago, tropical West Atlantic

Cleaner fishes are usually classified as obligate or facultative cleaners according to their diet and the extent to which their nutritional requirements in the different ontogenetic stages are gained from cleaning. While obligate cleaners clean throughout their lives and ingest mainly food taken from the clients` body surface, facultative cleaners clean only as juveniles and have a broader diet. In addition, some facultative cleaners may experience a relatively higher predation risk, and thus rarely interact with piscivorous fishes. Despite these acknowledged differences, there are very few studies that compare cleaning activity of obligate and facultative cleaners within the same area. Cleaning activity of the obligate cleaner goby Elacatinus cf. randalli and the facultative cleaner wrasse Thalassoma noronhanum were comparatively examined at Fernando de Noronha Archipelago, tropical West Atlantic. The client assemblage attended by the two cleaners differed, as the goby attended a slightly greater diversity of species (22), mostly piscivores and zoobenthivores, and the wrasse attended fewer species (19), mostly planktivores. Chromis multilineata was the most common client species of both cleaners, although body size (which is expected to be positively correlated to clients` ectoparasite load) of C. multilineata individuals attended by the goby was larger than that of the individuals attended by the wrasse. Despite such differences, T. noronhanum showed a surprisingly species-rich client assemblage when compared with other cleaners of the genus Thalassoma. In addition, the frequency and time spent on cleaning interactions, as well as the number of client species attended per 10-min period, was similar for both cleaner species, which indicate that they have important yet complimentary ecological roles in the reef community at Fernando de Noronha Archipelago.

Genetic diversity of heat-labile toxin expressed by enterotoxigenic Escherichia coli strains isolated from humans

The natural diversity of the eft operons, encoding the heat-labile toxin LT-I (LT), carried by enterotoxigenic Escherichia coli (ETEC) strains isolated from humans was investigated. For many years, LT was supposed to be represented by a rather conserved toxin, and one derivative, produced by the reference H10407 strain, was intensively studied either as a virulence factor or as a vaccine adjuvant. Amplicons encompassing the two LT-encoding genes (eltA and eltB) of 51 human-derived ETEC strains, either LT+ (25 strains) only or LT+/ST+ (26 strains), isolated from asymptomatic (24 strains) or diarrheic (27 strains) subjects, were subjected to restriction fragment length polymorphism (RFLP) analysis and DNA sequencing. Seven polymorphic RFLP types of the H10407 strain were detected with six (BsaI, DdeI, HhaI, HincII, HphI, and MspI) restriction enzymes. Additionally, the single-nucleotide polymorphic analysis revealed 50 base changes in the eft operon, including 21 polymorphic sites at eltA and 9 at eltB. Based on the deduced amino acid sequences, 16 LT types were identified, including LT1, expressed by the H10407 strain and 23 other strains belonging to seven different serotypes, and LT2, expressed by 11 strains of six different serotypes. In vitro experiments carried out with purified toxins indicated that no significant differences in GM1-binding affinity could be detected among LT1, LT2, and LT4. However, LT4, but not other toxin types, showed reduced toxic activities measured either in vitro with cultured cells (Y-1 cells) or in vivo in rabbit ligated ileal loops. Collectively, these results indicate that the natural diversity of LTs produced by wild-type ETEC strains isolated from human hosts is considerably larger than previously assumed and may impact the pathogeneses of the strains and the epidemiology of the disease.

Functional Diversity of Heat-labile Toxins (LT) Produced by Enterotoxigenic Escherichia coli

Heat-labile toxins (LTs) have ADP-ribosylation activity and induce the secretory diarrhea caused by enterotoxigenic Escherichia coli (ETEC) strains in different mammalian hosts. LTs also act as adjuvants following delivery via mucosal, parenteral, or transcutaneous routes. Previously we have shown that LT produced by human-derived ETEC strains encompass a group of 16 polymorphic variants, including the reference toxin (LT1 or hLT) produced by the H10407 strain and one variant that is found mainly among bacterial strains isolated from pigs (LT4 or pLT). Herein, we show that LT4 ( with six polymorphic sites in the A (K4R, K213E, and N238D) and B (S4T, A46E, and E102K) subunits) displays differential in vitro toxicity and in vivo adjuvant activities compared with LT1. One in vitro generated LT mutant (LTK4R), in which the lysine at position 4 of the A subunit was replaced by arginine, showed most of the LT4 features with an similar to 10-fold reduction of the cytotonic effects, ADP-ribosylation activity, and accumulation of intracellular cAMP in Y1 cells. Molecular dynamic studies of the A subunit showed that the K4R replacement reduces the N-terminal region flexibility and decreases the catalytic site crevice. Noticeably, LT4 showed a stronger Th1-biased adjuvant activity with regard to LT1, particularly concerning activation of cytotoxic CD8(+) T lymphocytes when delivered via the intranasal route. Our results further emphasize the relevance of LT polymorphism among human-derived ETEC strains that may impact both the pathogenicity of the bacterial strain and the use of these toxins as potential vaccine adjuvants.

Limited global diversity of the Plasmodium vivax merozoite surface protein 4 gene

Merozoite surface proteins (MSPs) of the malaria parasites are major candidates for vaccine development targeting asexual blood stages. However, the diverse antigenic repertoire of these antigens that induce strain-specific protective immunity in human is a major challenge for vaccine design and often determines the efficacy of a vaccine. Here we further assessed the genetic diversity of Plasmodium vivax MSP4 (PvMSP4) protein using 195 parasite samples collected mostly from Thailand, Indonesia and Brazil. Overall, PvMSP4 is highly conserved with only eight amino acid substitutions. The majority of the haplotype diversity was restricted to the two short tetrapeptide repeat arrays in exon 1 and 2, respectively. Selection and neutrality tests indicated that exon 1 and the entire coding region of PvMSP4 were under purifying selection. Despite the limited nucleotide polymorphism of PvMSP4, significant genetic differentiation among the three major parasite populations was detected. Moreover, microgeographical heterogeneity was also evident in the parasite populations from different endemic areas of Thailand. (C) 2009 Elsevier B.V. All rights reserved.

Diversity of Somatic Coliphages in Coastal Regions with Different Levels of Anthropogenic Activity in Sao Paulo State, Brazil

Bacteriophages are the most abundant and genetically diverse viruses on Earth, with complex ecology in both quantitative and qualitative terms. Somatic coliphages (SC) have been reported to be good indicators of fecal pollution in seawater. This study focused on determining the concentration of SC and their diversity by electron microscopy of seawater, plankton, and bivalve samples collected at three coastal regions in Sao Paulo, Brazil. The SC counts varied from < 1 to 3.4 x 103 PFU/100 ml in seawater (73 samples tested), from < 1 to 4.7 x 10(2) PFU/g in plankton (46 samples tested), and from < 1 to 2.2 x 10(1) PFU/g in bivalves (11 samples tested). In seawater samples, a relationship between the thermotolerant coliforms and Escherichia coli and SC was observed at the three regions (P = 0.0001) according to the anthropogenic activities present at each region. However, SC were found in plankton samples from three regions: Baixada Santista (17/20), Canal de Sao Sebastiao (6/14), and Ubatuba (3/12). In seawater samples collected from Baixada Santista, four morphotypes were observed: A1 (4.5%), B1 (50%), C1 (36.4%), and D1 (9.1%). One coliphage, Siphoviridae type T1, had the longest tail: between 939 and 995 nm. In plankton samples, Siphoviridae (65.8%), Podoviridae (15.8%), Microviridae (15.8%), and Myoviridae (2.6%) were found. In bivalves, only the morphotype B1 was observed. These SC were associated with enteric hosts: enterobacteria, E. coli, Proteus, Salmonella, and Yersinia. Baixada Santista is an area containing a high level of fecal pollution compared to those in the Canal de Sao Sebastiao and Ubatuba. This is the first report of coliphage diversity in seawater, plankton, and bivalve samples collected from Sao Paulo coastal regions. A better characterization of SC diversity in coastal environments will help with the management and evaluation of the microbiological risks for recreation, seafood cultivation, and consumption.