Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.     

High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities

Background and Aims

Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus.

Methods

Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus [‘Tapidor’ × ‘Ningyou 7’ (TNDH)] using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP.

Key Results

In general, root and biomass traits were highly correlated under LP and HP conditions. ‘Ningyou 7’ had greater LRL, LRN and LRD than ‘Tapidor’, at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06.

Conclusions

High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.     

Microbial quality of soil from the Pampa biome in response to different grazing pressures

The aim of this study was to evaluate the impact of different grazing pressures on the activity and diversity of soil bacteria. We performed a long-term experiment in Eldorado do Sul, southern Brazil, that assessed three levels of grazing pressure: high pressure (HP), with 4% herbage allowance (HA), moderate pressure (MP), with 12% HA, and low pressure (LP), with 16% HA. Two reference areas were also assessed, one of never-grazed native vegetation (NG) and another of regenerated vegetation after two years of grazing (RG). Soil samples were evaluated for microbial biomass and enzymatic (β-glucosidase, arylsulfatase and urease) activities. The structure of the bacterial community and the population of diazotrophic bacteria were evaluated by RFLP of the 16S rRNA and nifH genes, respectively. The diversity of diazotrophic bacteria was assessed by partial sequencing of the 16S rDNA gene. The presence of grazing animals increased soil microbial biomass in MP and HP. The structures of the bacterial community and the populations of diazotrophic bacteria were altered by the different grazing managements, with a greater diversity of diazotrophic bacteria in the LP treatment. Based on the characteristics evaluated, the MP treatment was the most appropriate for animal production and conservation of the Pampa biome.     

Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows?

It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log₁₀ copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.     

Increased dietary protein elevates plasma uric acid and is associated with decreased oxidative stress in rapidly-growing broilers

Uric acid is an important antioxidant and methods to elevate its plasma concentration may be important in animal health. In a first study, the effect of dietary protein on plasma uric acid (PUA) and glucose concentrations were determined in 3-week-old chicks. Twenty-four broiler chicks were randomly assigned to four diets: a commercial control diet (C, 20% crude protein), low protein (LP) containing 10% casein, medium protein (MP) containing 20% casein or high protein (HP) containing 45% casein for a 3-week experiment. PUA concentration increased (P<0.05) in chicks fed HP diet and declined (P<0.05) in chicks fed LP while plasma glucose concentrations were lower (P<0.05) in chicks fed the LP diet at the end of the study. In a second study, PUA and leukocyte oxidative activity (LOA) were determined in broilers fed C, LP, MP or HP diets for 4 weeks. As in the first study, dietary protein directly affected PUA concentrations. In birds consuming HP diets, PUA was negatively correlated (P=0.06) with lowered LOA. These data support the view that increases in dietary protein can increase PUA concentrations, which can ameliorate oxidative stress.     

闽江口芦苇沼泽湿地土壤产甲烷菌群落结构的垂直分布

应用PCR-RFLP技术及测序分析对闽江口芦苇湿地土壤产甲烷菌群落结构的垂直分布特征进行了研究。在构建的6个克隆文库中,每个克隆文库随机挑选100个克隆进行菌落PCR验证,共得到591个阳性克隆。PCR产物经限制性内切酶MspⅠ进行RFLP分析后得到37个不同的分类操作单元(OTUs)。对37个克隆子进行了序列测定,与GenBank数据库中的序列进行比对,最近相似性在91%—99%之间。RFLP分析和系统发育分析表明,闽江口芦苇湿地土壤中产甲烷菌群落包括3大类群:甲烷杆菌目(Methanobacteriales)、甲烷微菌目(Methanomirobiales)和甲烷八叠球菌目(Methanosarcinales)。不同土壤深度中产甲烷菌群落的分布呈现出不同的特征。土壤表层(0—10 cm)优势产甲烷菌类群为Methanoregula,约占76%;10—20 cm土层主要的产甲烷菌类群为Methanolinea和Methanoregula,分别约占23%和29%;20—30cm土层优势的产甲烷菌类群为Methanolinea,约占66%。Shannon指数(H’)和Simpson多样性指教(D)表明,10—20cm土层产甲烷菌多样性高于土壤表层(0—10 cm)和20—30 cm土层。37个测序OTUs中有26个OTUs属于不可培养的产甲烷菌序列,表明闽江口芦苇湿地土壤中存在大量不可培养的产甲烷菌。     

Diagnostic challenges of single plaque-like lesion paucibacillary leprosy

The diagnosis of single-lesion paucibacillary leprosy remains a challenge. Reviews by expert dermatopathologists and quantitative polymerase chain reaction (qPCR) results obtained from 66 single-plaque biopsy samples were compared. Histological findings were graded as high (HP), medium (MP) or low (LP) probability of leprosy or other dermatopathy (OD). Mycobacterium leprae-specific genes were detected using qPCR. The biopsies of 47 out of 57 clinically diagnosed patients who received multidrug therapy were classified as HP/MP, eight of which were qPCR negative. In the LP/OD (n = 19), two out of eight untreated patients showed positive qPCR results. In the absence of typical histopathological features, qPCR may be utilised to aid in final patient diagnosis, thus reducing overtreatment and delay in diagnosis.     

Early oocyte penetration can predict the efficiency of bovine embryo production in vitro

The aim of this work was to characterize oocyte fertilization and embryo cleavage in nine AI bulls to find parameters suitable for prediction of in vitro fertility. According to the d8 blastocysts rate, they were categorized as high, medium and low productive (HP, MP and LP, mean: 25.4, 21.0 and 13.6% respectively) bulls. For these categories, oocyte penetration and fertilization efficiency were assessed at 6 and 18 hours post insemination (hpi), respectively. Some presumptive zygotes were cultured and cleaved and fast-cleaved embryo rates were checked at 44 hpi. The penetration rate was significantly higher for HP bulls than for MP and LP bulls (67.9 versus 50.3 and 33.1%; p<0.01). The syngamy rate was significantly higher for HP bulls than for MP and LP bulls (21.4 versus 10.2 and 5.7%; p<0.05). Conversely, no significant differences in fertilization rates were found among HP, MP and LP bulls. The cleavage rate was significantly higher for HP than LP bulls (82.4 versus 74.4%; p<0.01). The fast cleavage rate was significantly higher for both HP and MP bulls, as compared with LP bulls (82.1 and 84.7 versus 73.5%; p<0.01). A strong correlation was found between blastocyst production and penetration (r=0.803), syngamy (r=0.826), cleavage (r=0.635) and fast cleavage (r=0.709). In conclusion, all the evaluated parameters showed a predictive value, the most significant being early penetration and syngamy.     

Dietary carbohydrate composition modifies the milk N efficiency in late lactation cows fed low crude protein diets

Nitrogen emissions from dairy cows can be readily decreased by lowering the dietary CP concentration. The main objective of this work was to test whether the milk protein yield reduction associated with low N intakes could be partially compensated for by modifying the dietary carbohydrate composition (CHO). The effects of CHO on digestion, milk N efficiency (milk N/N intake; MNE) and animal performance were studied in four Jersey cows fed 100% or 80% of the recommended protein requirements using a 4×4 Latin square design. Four iso-energetic diets were formulated to two different CHO sources (starch diets with starch content of 34.3% and NDF at 32.5%, and fiber diets with starch content of 5.5% and NDF at 49.1%) and two CP levels (Low=12.0% and Normal=16.5%). The apparent digestible organic matter intake (DOMI) and the protein supply (protein digestible in the small intestine; PDIE) were similar between starch and fiber diets. As planned, microbial N flow (MNF) to the duodenum, estimated from the urinary purine derivatives (PD) excretion, was similar between Low and Normal CP diets. However, the MNF and the efficiency of microbial synthesis (g of microbial N/kg apparently DOMI) were higher for starch v. fiber diets. Milk and milk N fractions (CP, true protein, non-protein N (NPN)) yield were higher for starch compared with fiber diets and for Normal v. Low CP diets. Fecal N excretion was similar across dietary treatments. Despite a higher milk N ouput with starch v. fiber diets, the CHO modified neither the urinary N excretion nor the milk urea-N (MUN) concentration. The milk protein yield relative to both N and PDIE intakes was improved with starch compared with fiber diets. Concentrations of β-hydroxybutyrate, urea and Glu increased and those of glucose and Ala decreased in plasma of cows fed starch v. fiber diets. On the other hand, plasma concentration of albumin, urea, insulin and His increased in cows fed Normal compared with Low CP diets. This study showed that decreasing the dietary CP proportion from 16.5% to 12.0% increases and decreases considerably the MNE and the urinary N excretion, respectively. Moreover, present results show that at similar digestible OM and PDIE intakes, diets rich in starch improves the MNE and could partially compensate for the negative effects of Low CP diets on milk protein yield.     

Site History and Edaphic Features Override the Influence of Plant Species on Microbial Communities in Restored Tidal Freshwater Wetlands

Restored wetland soils differ significantly in physical and chemical properties from their natural counterparts even when plant community compositions are similar, but effects of restoration on microbial community composition and function are not well understood. Here, we investigate plant-microbe relationships in restored and natural tidal freshwater wetlands from two subestuaries of the Chesapeake Bay. Soil samples were collected from the root zone of Typha latifolia, Phragmites australis, Peltandra virginica, and Lythrum salicaria. Soil microbial composition was assessed using 454 pyrosequencing, and genes representing bacteria, archaea, denitrification, methanogenesis, and methane oxidation were quantified. Our analysis revealed variation in some functional gene copy numbers between plant species within sites, but intersite comparisons did not reveal consistent plant-microbe trends. We observed more microbial variations between plant species in natural wetlands, where plants have been established for a long period of time. In the largest natural wetland site, sequences putatively matching methanogens accounted for ∼17% of all sequences, and the same wetland had the highest numbers of genes coding for methane coenzyme A reductase (mcrA). Sequences putatively matching aerobic methanotrophic bacteria and anaerobic methane-oxidizing archaea (ANME) were detected in all sites, suggesting that both aerobic and anaerobic methane oxidation are possible in these systems. Our data suggest that site history and edaphic features override the influence of plant species on microbial communities in restored wetlands.     

Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-¹³C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of ¹³C into DNA was detectable at in situ acetate concentrations (∼7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the ¹³C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.     

Are dairy cows with a more reactive temperament less efficient in energetic metabolism and do they produce more enteric methane?

It remains unknown whether dairy cows with more reactive temperament produce more enteric methane (CH₄) and are less bioenergetically efficient than the calmer ones. The objectives of this study were (a) to evaluate the relationship between cattle temperament assessed by traditionally used tests with energetic metabolism and enteric CH₄ emissions by crossbred dairy cows; (b) to assess how cows’ restlessness in respiration chambers affects energetic metabolism and enteric CH₄ emissions. Temperament indicators were evaluated for 28 primiparous F1 Holstein-Gyr cows tested singly in the handling corral (entrance time, crush score, flight speed, and flight distance) and during milking (steps, kicks, defecation, rumination, and kick the milking cluster off). Cows’ behaviors within respiration chambers were also recorded for each individual kept singly. Digestibility and calorimetry trials were performed to obtain energy partitioning and CH₄ measures. Cows with more reactive temperament in milking (the ones that kicked the milking cluster off more frequently) spent 25.24% less net energy on lactation (P = 0.04) and emitted 36.77% more enteric CH₄/kg of milk (P = 0.03). Furthermore, cows that showed a higher frequency of rumination at milking parlor allocated 57.93% more net energy for milk production (P < 0.01), spent 50.00% more metabolizable energy for milk production (P < 0.01) and 37.10% less CH₄/kg of milk (P = 0.04). Regarding the handling temperament, most reactive cows according to flight speed, lost 29.16% less energy as urine (P = 0.05) and tended to have 14.30% more enteric CH₄ production (P = 0.08), as well as cows with a lower entrance time (most reactive) that also lost 13.29% more energy as enteric CH₄ (P = 0.04). Temperament and restless behavior of Holstein-Gyr cows were related to metabolic efficiency and enteric CH₄ emissions. Cows’ reactivity and rumination in the milking parlor, in addition to flight speed and entrance time in the squeeze chute during handling in the corral, could be useful measures to predict animals more prone to metabolic inefficiency, which could negatively affect the sustainability of dairy systems.     

Methane dynamics across wetland plant species

We examined patterns of methane flux, plant biomass, and microbial methanogenic populations in nine wetland plant species. Methane dynamics varied across plant functional groupings, with patterns distinctive among forbs, clonal dominants, and tussock/clump-forming graminoids. Carex stricta and Scirpus atrovirens showed the highest emissions (31.7 and 20.6 mg CH₄-C m⁻² h⁻¹), followed by other tussock- or clump-forming graminoids that averaged 11.0 mg CH₄-C m⁻² h⁻¹ (Scirpus cyperinus, Glyceria striata, and Juncus effusus). The clonal dominants (Phalaris arundinacea and Typha angustifolia) had the lowest methane emissions (1.3 and 3.4 mg CH₄-C m⁻² h⁻¹) of all seven graminoid species, and the forbs (Mimulus ringens and Verbena hastata) emitted no detectable methane flux from their leaves. In general, methane emissions decreased with greater plant biomass. Terminal restriction fragment analysis (T-RFLP) of archaeal 16S rRNA revealed that the structure of the soil methanogen communities isolated from plant rhizospheres had no effect on methane flux. The relative proportions of the different terminal fragments were not correlated with either methane emissions or plant biomass. Methanogen populations from J. effusus soils were dominated by acetoclastic archaea of the Methanosarcinaceae and Methanosaetaceae families, while all other graminoid soils were colonized primarily by hydrogenotrophic archaea of the Methanobacteriaceae family. The results indicate that plant functional groups and plant biomass are useful in predicting methane flux differences across plant species, while soil methanogen community structure showed no distinguishable patterns.     

Identifying the limitations for growth in low performing piglets from birth until 10 weeks of age

The evolution of hyper-prolific pig breeds has led to a higher within-litter variation in birth weight and in BW gain during the nursery phase. Based on an algorithm developed in previous research, two populations from a pool of 368 clinically healthy piglets at 6 weeks of age were selected: a low (LP) and a high (HP) performing population and their development was monitored until the end of the nursery phase (10 weeks of age). To understand the cause of the variation in growth between these populations we characterized the LP and HP piglets in terms of body morphology, behaviour, voluntary feed intake, BW gain, and apparent total tract and ileal nutrient digestibility. Piglets were housed individually and were fed a highly digestible diet. At selection, 6 weeks of age, the BW of LP and HP piglets were 6.8±0.1 and 12.2±0.1 kg, respectively. Compared with the LP piglets the HP piglets grew faster (203 g/day), ate more (275 g/day) from 6 to 10 weeks of age and were heavier at 10 weeks (30.0 v. 18.8 kg, all P<0.01). Yet, the differences in average daily gain and average daily feed intake disappeared when compared per kg BW^0.75. Assuming similar maintenance requirements per kg BW^0.75 the efficiency of feed utilization above maintenance was 0.1 g/g lower for the LP piglets (P=0.09).The gain : feed ratio was similar for both groups. LP piglets tended to take more time to touch a novel object (P=0.10), and spent more time eating (P<0.05). At 10 weeks, LP piglets had a higher body length and head circumference relative to BW (P<0.01). Relative to BW, LP had a 21% higher small intestine weight; 36% longer length, and relative to average FI, the small intestinal weight was 4 g/kg higher (both P=<0.01). Apparent total tract and ileal dry matter, N and gross energy digestibility were similar between groups (P>0.10). We concluded that the low performance of the LP piglets was due to their inability to engage compensatory gain or compensatory feed intake as efficiency of nutrient utilization and feed intake per kg BW^0.75 was unaffected. LP piglets tend to be more fearful towards novel objects. The morphological comparisons, increased body length and head circumference relative to BW imply that LP piglets have an increased priority for skeletal growth.     

Heritability and repeatability of milk lactose and its relationships with traditional milk traits,somatic cell score and freezing point in Holstein cows

Lactose percentage (LP) in milk is currently determined in most herd-testing schemes, and globally, it is usually routinely recorded in the framework of the official milk recording procedures. However, few studies have investigated the phenotypic and genetic variability of this component. Data used in the present paper consisted of 59 811 test-day records from 4355 Holstein cows in 266 herds. Heritabilities of LP and lactose yield (LY) were estimated through single-trait repeatability animal models, whereas genetic and phenotypic correlations of LP and LY with milk composition and production traits, somatic cell score and milk freezing point were estimated using bivariate models. Fixed effects included in the analyses were herd-test-date, season of calving, parity, stage of lactation and the interaction between parity and stage of lactation. Random effects were animal additive genetic, within and across lactation permanent environment and the residual. Lactation curves of LP and LY increased from parturition to the peak of lactation and decreased thereafter, mirroring the typical curve of milk yield. Lactose percentage was greater in first- than later-parity cows. Heritabilities of LP and LY were 0.43±0.03 and 0.14±0.02, respectively, and LP and protein percentage were the most repeatable traits. Genetic correlations (r_a) of LP with somatic cell score, LY and milk freezing point were −0.22±0.08, 0.28±0.08 and −0.46±0.05, respectively. Genetic relationships of LY with milk yield (r_a=0.97±0.00), fat percentage (r_a=−0.71±0.06), protein percentage (r_a=−0.57±0.06) and protein yield (r_a=0.64±0.06) were moderate to strong. Results suggest that milk LP could be considered in breeding strategies to accelerate the gain of correlated low heritable traits. Further research is needed to evaluate the feasibility of including LP in the selection index of Italian Holstein population to address country-specific needs and market demands.     

Comparative Genomic Analysis Reveals 2-Oxoacid Dehydrogenase Complex Lipoylation Correlation with Aerobiosis in Archaea

Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.     

Archaea of the Miscellaneous Crenarchaeotal Group are abundant,diverse and widespread in marine sediments

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.     

Detection of QTL for phosphorus efficiency at vegetative stage in Brassica napus

Phosphorus (P) deficiency in soils is a major limiting factor for plant growth worldwide. Plants have developed adaptive strategies in response to P deficiency. The objective of this study was to map quantitative trait loci (QTL) for P efficiency using a recombinant inbred (RI) population consisting of 124 lines derived from a cross between Brassica napus P-inefficient cv. B104-2 and P-efficient cv. Eyou Changjia. Six traits (shoot dry weight, root dry weight, root/shoot ratio, P concentration, shoot P uptake and shoot P use efficiency) at vegetative stage were examined under high P (HP, 1 mM) and low P (LP, 5 ??M) conditions during three separate experimental trial periods. Their relative values (i.e., the ratio of a trait value under the LP condition to that under the HP condition) of these six traits were also determined. Eyou Changjia produced more biomass and acquired more P under the LP condition and, thus, had a higher relative dry weight and relative P uptake than B104-2, indicating Eyou Changjia was high P efficiency. A total of 71 QTL were detected on 13 linkage groups, including 28 QTL under the LP condition, 22 QTL under the HP condition and 21 QTL for relative traits. Nineteen and nine QTL were specific for the LP and HP conditions, respectively, suggesting that different mechanisms existed under the two P condition. Twelve of the twenty-one QTL for relative traits co-localized with QTL identified under the two P conditions. In addition, 18 orthologous genes involved in the P metabolic pathway of Arabidopsis were in silico mapped to the QTL confidence intervals identified in B. napus by comparative genomic analysis. These QTL and their corresponding candidate genes should be further investigated to better understand P efficiency in B. napus.     

Herbage intake,methane emissions and animal performance of steers grazing dwarf elephant grass v. dwarf elephant grass and peanut pastures

Management strategies for increasing ruminant legume consumption and mitigating methane emissions from tropical livestock production systems require further study. The aim of this work was to evaluate the herbage intake, animal performance and enteric methane emissions of cattle grazing dwarf elephant grass (DEG) (Pennisetum purpureum cv. BRS Kurumi) alone or DEG with peanut (Arachis pintoi cv. Amarillo). The experimental treatments were the following: DEG pastures receiving nitrogen fertilization (150 kg N/ha as ammonium nitrate) and DEG intercropped with peanut plus an adjacent area of peanut that was accessible to grazing animals for 5 h/day (from 0700 to 1200 h). The animals grazing legume pastures showed greater average daily gain and herbage intake, and shorter morning and total grazing times. Daily methane emissions were greater from the animals grazing legume pastures, whereas methane emissions per unit of herbage intake did not differ between treatments. Allowing animals access to an exclusive area of legumes in a tropical grass-pasture-based system can improve animal performance without increasing methane production per kg of dry matter intake.     

Biochemical cycling in the rhizosphere having an impact on global change

Changes in chemical properties in soil around plant roots influence many microbial processes, including those having an impact on greenhouse gas emissions. To potentially mitigate these emissions according to the Kyoto protocol, knowledge about how and where these gases are produced and consumed in soils is required. In this review, we focus on the greenhouse gases nitrous oxide and methane, which are produced by nitrifying and denitrifying prokaryotes and methanogenic archaea, respectively. After describing the microbial processes involved in production and consumption of nitrous oxide and methane and how they can be affected in the rhizosphere, we give an overview of nitrous oxide and methane emissions from the rhizosphere and soils and sediments with plants. We also discuss strategies to mitigate emissions from the rhizosphere and consider possibilities for carbon sequestration.