Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea

Ruminal methanogens, bacteria and ciliate protozoa of Svalbard reindeer grazing natural pastures in October (late fall) and April (late winter) were investigated using molecular-based approaches. The appetite of the Svalbard reindeer peaks in August (summer) and is at its lowest in March (winter). Microbial numbers, quantified by real-time PCR, did not change significantly between October and April, when food intakes are at similar levels, although the numbers of methanogens tended to be higher in October ( P =0.074), and ciliate numbers tended to be higher in April ( P= 0.055). Similarly, no change was detected in the bacterial and protozoal population composition by rRNA gene-based denaturing gradient gel electrophoresis analysis. Dominant methanogens were identified using a 16S rRNA gene library (97 clones) prepared from pooled PCR products from reindeer on October pasture ( n =5). Eleven of the 22 distinct operational taxonomic units (OTUs) generated exhibited a high degree of sequence similarity to methanogens affiliated with Methanobacteriales (eight OTUs), Methanomicrobiales (one OTU) and Methanosarcinales (two OTUs). The remaining 11 OTUs (53% of the clones) were associated with a cluster of uncultivated ruminal archaea. This study has provided important insights into the rumen microbiome of a high-arctic herbivorous animal living under harsh nutritional conditions, and evidence suggesting that host type affects the population size of ruminal methanogens.     

Changes in microbial community structure, methanogenesis and rumen fermentation in response to saponin-rich fractions from different plant materials

Aims:  Investigation of the effects of saponin-rich fractions on rumen fermentation, methane production and the microbial community.
Methods and Results:  Saponins were extracted from Carduus , Sesbania and Knautia leaves and fenugreek seeds. Two levels of saponin-rich fractions with a substrate were incubated using the Hohenheim gas method. Methane was measured using an infrared-based methane analyser and microbial communities using quantitative PCR. On addition of saponin-rich fractions, methane and short-chain fatty acid production was not affected. The protozoal counts decreased by 10–39%. Sesbania saponins decreased methanogen population by 78%. Decrease in ruminal fungal population (20–60%) and increase in Fibrobacter succinogenes (21–45%) and Ruminococcus flavefaciens (23–40%) were observed.
Conclusions:  The saponins evaluated possessed anti-protozoal activity; however, this activity did not lead to methane reduction. Fenugreek saponins seemed to have potential for increasing rumen efficiency. The saponins altered the microbial community towards proliferation of fibre-degrading bacteria and inhibition of fungal population.
Significance and Impact of the Study:  The uni-directional relationship between protozoal numbers and methanogenesis, as affected by saponins, is not obligatory. All saponins might not hold promise for decreasing methane production from ruminants.     

Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island,Japan

A total of 32 wild Hokkaido sika deer (Cervus nippon yesoensis) were shot (13 in summer, nine in autumn and 10 in winter) in the Syari district, Shiretoko Peninsula of Hokkaido Island, Japan. The ingested foods, rumen fermentation parameters and microbes were determined to evaluate digestive strategy and food availability in each season. Ingested foods and ruminal characteristics greatly varied by season. Rumen digesta mainly comprised of graminoids in summer, graminoids and agricultural products in autumn, and bark and twigs in winter. Rumen pH showed seasonal differences (P<0.05) and was lowest in summer, highest in winter, and intermediate in autumn, reflecting the seasonal differences in ruminal concentration of total volatile fatty acids which were significantly lower (P<0.05) in winter than in summer and autumn. Acetate proportions were significantly higher in winter than in other seasons (P<0.05), while the opposite trend was seen in proportions of propionate and butyrate. Rumen ammonia levels showed significant seasonal differences (P<0.05), decreasing from summer to autumn to winter. Rumen protozoa levels in autumn and winter decreased to 28 and 10% of the levels observed in summer, respectively (P<0.05 for both). The rumen bacteria level in winter was lower (P<0.05) than that in autumn, but no difference was seen for the other seasonal comparisons. Gram negative cocci were present in significantly higher proportions in winter than in other seasons (P<0.05), while Gram negative curved rods were less frequently observed in winter (P<0.05). Based on these results, wild sika deer in this area are shown to survive with rumen microbial populations altered with the dietary conditions that vary greatly by season.     

Effect of complete feed blocks or grazing and supplementation of lambs on performance, nutrient utilisation, rumen fermentation and rumen microbial enzymes

A study to compare two feeding systems, stall feeding (SF) and grazing plus supplementation (GR) was carried out, based on intake, performance and rumen fermentation characteristics of lambs. While SF animals received ad libitum complete feed blocks (CFB), GR animals were allowed grazing for 8 h on a pasture and supplemented with concentrate mixture at 250 g per head per day. Intake in grazing animals was determined using chromium III oxide as internal marker. Intake of dry matter (DM), crude protein (CP) and organic matter (OM) were higher ( P < 0.01) in SF than in GR animals. Similarly, digestibility of OM, CP and energy were higher ( P < 0.01) in SF animals. Average daily gain in SF animals (101 g) was significantly ( P < 0.01) higher than in GR animals (78 g) but total wool yield was similar for the two groups (856 g, SF; 782 g, GR). The pH of the rumen content, concentration of total volatile fatty acids and total activities of carboxymethyl cellulase, xylanase and esterase in the rumen liquor were similar. The concentrations (mg/dl) of total nitrogen (125, SF; 63, GR) and NH₃-nitrogen (42, SF; 31, GR) were higher in SF animals than that of GR animals. A significantly higher activity ( P < 0.05) of microcrystalline cellulase (24.5 v. 7.7 units) and lower activity ( P < 0.05) of protease (309 v. 525 units), was observed in the rumen of SF animals than in GR animals. SF animals could therefore harness more energy through degradation of plant cell walls thus reducing breakdown of plant proteins as gluconeogenic source. The SF system of feeding where CFB was offered to sheep appeared superior to GR in terms of intake, nutrient utilisation and animal performance. Therefore the SF feeding system where CFB are offered to animals can be advocated as an alternative to grazing and supplementation feeding strategy for sheep production, especially where the pastures are highly eroded and need resting for regeneration or curing. The CFB feeding can also be adopted under adverse conditions like drought and famine, a common phenomenon in arid and semiarid conditions.     

The characterization of lactic acid producing bacteria from the rumen of dairy cattle grazing on improved pasture supplemented with wheat and barley grain

Aims:  To identify and characterize the major lactic acid bacteria in the rumen of dairy cattle grazing improved pasture of rye grass and white clover and receiving a maize silage and grain supplement with and without virginiamycin.
Methods and Results:  Eighty-five bacterial isolates were obtained from the rumen of 16 Holstein-Friesian dairy cows. The isolates were initially grouped on the basis of their Gram morphology and by restriction fragment length polymorphism analysis of the PCR amplified 16S rDNA. A more definitive analysis was undertaken by comparing the 16S rDNA sequences. Many of the isolates were closely related to other previously characterized rumen bacteria, including Streptococcus bovis, Lactobacillus vitulinus , Butyrivibrio fibrisolvens , Prevotella bryantii and Selenomonas ruminantium . The in vitro production of l - and/or d -lactate was seen with all but five of the isolates examined, many of which were also resistant to virginiamycin.
Conclusion:  Supplementation of grain with virginiamycin may reduce the risk of acidosis but does not prevent its occurrence in dairy cattle grazing improved pasture.
Significance and Impact of the Study:  This study shows that lactic acid production is caused, not only by various thoroughly researched types of bacteria, but also by others previously identified in the rumen but not further characterized.     

Dissimilatory microbial sulfur and methane metabolism in the water column of a shallow meromictic lake

Lake Harutori is a brackish meromictic lake with a steep physicochemical gradient in shallow water. Anoxic water below the chemocline has been characterized by high concentrations of sulfide (>10 mM) and methane (>1.5 mM). Previously, we reported that uncultured bacteria in the SEEP-SRB1 group were major sulfate reducers in the lake [21], but knowledge of sulfur oxidation and methane metabolism was scarce. In this current study, the Lake Harutori microbial community structure in the mixolimnion (at depths of 1.5 m and 3.0 m), upper chemocline (3.5 m), and monimolimnion (4.5 m) was further investigated by 16S rRNA gene amplicon sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Reads of type I and II methanotrophs were retrieved mainly from 3.5 m and above. Methanotrophic bacteria detected by CARD-FISH accounted for 3.1% of DAPI-stained cells at 3.5 m. Detection frequencies of reads affiliated with the genera Sulfurimonas and Thiomicrorhabdus, which are known to comprise sulfur oxidizers, were relatively high at 3.5 m. Methanogenic archaeal reads were retrieved from the monimolimnion and they affiliated with the genus Methanosaeta. CARD-FISH counts indicated that the cells of Methanosaeta/Methanosarcina/Methanomicrobiales accounted for up to 0.8% of the DAPI-stained cells in the monimolimnion. On the other hand, many of the reads retrieved primarily from the monimolimnion were affiliated with phylogenetically novel uncultured groups.     

Effect of supplementing coconut or krabok oil,rich in medium-chain fatty acids on ruminal fermentation,protozoa and archaeal population of bulls

Medium-chain fatty acids (MCFA), for example, capric acid (C10:0), myristic (C14:0) and lauric (C12:0) acid, have been suggested to decrease rumen archaeal abundance and protozoal numbers. This study aimed to compare the effect of MCFA, either supplied through krabok (KO) or coconut (CO) oil, on rumen fermentation, protozoal counts and archaeal abundance, as well as their diversity and functional organization. KO contains similar amounts of C12:0 as CO (420 and 458 g/kg FA, respectively), but has a higher proportion of C14:0 (464 v. 205 g/kg FA, respectively). Treatments contained 35 g supplemental fat per kg DM: a control diet with tallow (T); a diet with supplemental CO; and a diet with supplemental KO. A 4th treatment consisted of a diet with similar amounts of MCFA (i.e. C10:0+C12:0+C14:0) from CO and KO. To ensure isolipidic diets, extra tallow was supplied in the latter treatment (KO+T). Eight fistulated bulls (two bulls per treatment), fed a total mixed ration predominantly based on cassava chips, rice straw, tomato pomace, rice bran and soybean meal (1.5% of BW), were used. Both KO and CO increased the rumen volatile fatty acids, in particular propionate and decreased acetate proportions. Protozoal numbers were reduced through the supplementation of an MCFA source (CO, KO and KO+T), with the strongest reduction by KO. Quantitative real-time polymerase chain reaction assays based on archaeal primers showed a decrease in abundance of Archaea when supplementing with KO and KO+T compared with T and CO. The denaturing gradient gel electrophoresis profiles of the rumen archaeal population did not result in a grouping of treatments. Richness indices were calculated from the number of DGGE bands, whereas community organization was assessed from the Pareto–Lorenz eveness curves on the basis of DGGE band intensities. KO supplementation (KO and KO+T treatments) increased richness and evenness within the archaeal community. Further research including methane measurements and productive animals should elucidate whether KO could be used as a dietary methane mitigation strategy.     

Life in the dark: metagenomic evidence that a microbial slime community is driven by inorganic nitrogen metabolism

Beneath Australia''s large, dry Nullarbor Plain lies an extensive underwater cave system, where dense microbial communities known as ‘slime curtains'' are found. These communities exist in isolation from photosynthetically derived carbon and are presumed to be chemoautotrophic. Earlier work found high levels of nitrite and nitrate in the cave waters and a high relative abundance of Nitrospirae in bacterial 16S rRNA clone libraries. This suggested that these communities may be supported by nitrite oxidation, however, details of the inorganic nitrogen cycling in these communities remained unclear. Here we report analysis of 16S rRNA amplicon and metagenomic sequence data from the Weebubbie cave slime curtain community. The microbial community is comprised of a diverse assortment of bacterial and archaeal genera, including an abundant population of Thaumarchaeota. Sufficient thaumarchaeotal sequence was recovered to enable a partial genome sequence to be assembled, which showed considerable synteny with the corresponding regions in the genome of the autotrophic ammonia oxidiser Nitrosopumilus maritimus SCM1. This partial genome sequence, contained regions with high sequence identity to the ammonia mono-oxygenase operon and carbon fixing 3-hydroxypropionate/4-hydroxybutyrate cycle genes of N. maritimus SCM1. Additionally, the community, as a whole, included genes encoding key enzymes for inorganic nitrogen transformations, including nitrification and denitrification. We propose that the Weebubbie slime curtain community represents a distinctive microbial ecosystem, in which primary productivity is due to the combined activity of archaeal ammonia-oxidisers and bacterial nitrite oxidisers.     

Diversity and dynamics of the bacterial community involved in pig manure biodegradation in a microbial fermentation bed system

Overproduction of livestock manures with unpleasant odors causes significant environmental problems. The microbial fermentation bed (MFB) system is considered an effective approach to recycling utilization of agricultural byproducts and pig manure (PM). To gain a better understanding of bacterial communities present during the degradation of PM in MFB, the PM bacterial community was evaluated at different fermentation stages using 16S rRNA high throughput sequencing technology. The heatmap plot clustered five samples into short-term fermentation stage of 0–10 days and long-term fermentation stage of 15–20 days. The most abundant OTUs at the phylum level were Firmicutes, Actinobacteria and Proteobacteria in the long-term fermentation stage of PM, whereas Firmicutes, Bacteroidetes, and Proteobacteria predominated in the short-term fermentation stage of PM. At the genus level, organic degradation strains, such as Corynebacterium, Bacillus, Virgibacillus, Pseudomonas, Actinobacteria, Lactobacillus, Pediococcus were the predominate genera at the long-term fermentation stage, but were found only rarely in the short-term fermentation stage. C/N ratios increased and the concentration of the unpleasant odor substance 3-hydroxy-5-methylisoxazole (3-MI) decreased with prolonged period of fermentation. Redundancy analysis (RDA) demonstrated that the relative abundance of Firmicutes, Actinobacteria, Acidobacteria and Proteobacteria had a close relationship with degradation of 3-MI and increasing C/N ratio. These results provide valuable additional information about bacterial community composition during PM biodegradation in animal husbandry.     

施氮肥对华北平原土壤氨氧化细菌和古菌数量及群落结构的影响

利用荧光定量PCR、末端限制性片段长度多样性(T-RFLP)和基因克隆文库技术,比较了4种施氮水平(不施氮肥,0 kg N/hm~2,CK;施低水平氮肥,75 kg N/hm~2,N1;施中水平氮肥,150 kg N/hm~2,N2;施高水平氮肥,225 kg N/hm~2,N3)下华北平原地区小麦季表层(0—20 cm)土壤总细菌、氨氧化细菌(AOB)和氨氧化古菌(AOA)的丰度和群落结构。结果表明,土壤总细菌、AOB和AOA数量分别在每克干土5.74×10~9—7.50×10~9、8.89×10~6—2.66×10~7和3.83×10~8—7.78×10~8之间。不同施氮量土壤AOA数量均高于AOB数量,AOA/AOB值在81.72—14.38之间。增施氮肥显著显著提高AOB数量(P0.05),对总细菌和AOA数量的影响不显著(P0.05)。与CK相比,处理N1、N2和N3中AOB数量分别提高了0.64、1.50和1.99倍。增施氮肥显著改变了AOB和AOA的群落结构,且不同施氮量处理中AOB群落结构差异更大。系统进化分析显示,施氮肥小麦土壤AOB主要为Nitrosospira属类群,分布在Cluster 3的两个分支中;AOA分布在Cluster S的4个分支中。相关性分析显示,AOB数量与全氮和铵态氮含量呈显著正相关关系,与土壤pH和碳氮比呈显著负相关关系(P0.05);AOA数量与硝态氮含量和土壤pH呈显著正相关关系,与铵态氮含量呈显著负相关关系(P0.05)。研究结果表明:增施氮肥可显著改变华北平原地区碱性土壤AOB数量与群落结构,该地区小麦土壤中AOB比AOA对氮肥响应更敏感。     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

Effects of the long-term application of inorganic fertilizers on microbial community diversity in rice-planting red soil as studied by using PCR-DGGE

The effects of the long-term application of inorganic fertilizers on microbial community diversity were investigated in a rice-planting soil derived from quaternary red clay in the Ecological Experimental Station of Red Soil, Chinese Academy of Sciences. After 13 years' application of different inorganic fertilizers for double rice crops, the community structure of bacteria, archaea, actinomycetes and fungi in the soil changed greatly. The similarity of the SSU rDNA DGGE patterns of these four kinds of microorganisms between the soil without rice-planting and the soil with rice-planting reached only 33% and 66%, respectively. The microbial community structure among treatments with NP, PK and NPK types of P fertilizers were more similar; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached a high range of 75%–81%. The microbial community structure between the treatment with N and K fertilizers (NK) and the treatment without inorganic fertilization (CK) with the treatments with P fertilizers differed greatly; the similarity of the SSU rDNA DGGE patterns of the four kinds of microorganisms under these treatments reached 69%–77% and 55%–77%, respectively. The results of this study provide a scientific basis for fertilizing and utilizing soil, protecting microbial diversity, and accomplishing the sustainable development of agroecology.     

低温沼气发酵优良菌系筛选及优势菌群分析

【目的】为获得低温沼气发酵高效菌系, 从张家口、承德和邯郸地区采集低温产气良好的沼气池中沼泥样品12份。【方法】以沼泥为接种源进行16 °C?5 °C阶段降温模拟沼气发酵试验, 对处理组HL2、ZG2、CW1及其相应的接种源HLA、ZGB、CWB进行DGGE分析。【结果】ZG2处理组模拟沼气发酵综合性能最优, 与其他处理组呈显著性差异; DGGE图谱显示, 被检测样品中古菌种属多样性丰富, 但图谱中代表优势种属条带的位置存在较大差异。通过16S rDNA克隆及测序分析, 样品中主要优势菌属为甲烷八叠球菌属、甲烷鬃毛菌属和甲烷粒菌属。【结论】DGGE图谱中代表甲烷八叠球菌属的条带是样品ZG2和ZGB中唯一重复出现的条带, 且未作为优势条带出现在其他样品中, 推测甲烷八叠球菌属与低温产沼气有密切相关性。     

An investigation of the relationship between fecal and rumen bacterial concentrations in sheep

With no acceptable method for collecting fresh rumen fluid from zoo ruminants, it was proposed that fecal bacterial concentrations may be correlated with rumen bacteria. If so, fecal bacterial concentrations could be used to study both the effects of diet on rumen bacteria as well as rumen abnormalities. Total and cellulolytic bacterial concentrations were determined in whole rumen contents and feces of sheep using a most‐probable‐number (MPN) assay. In a Latin square design, four crossbred ewes were fed diets of 100% long or chopped orchardgrass hay (OH) and 60% ground or whole shelled corn plus 40% chopped OH. In a second trial, the sheep were fed a pelleted complete feed at varying levels of intake i.e., control at 2.0% of body weight and at 1.8, 1.6, and 1.2% of body weight. Higher total rumen bacterial concentrations (P<0.01) were found on the high concentrate diets as compared with the high forage diets. Grinding the corn also increased total bacterial concentrations (P<0.05). Fecal concentrations of total bacteria were higher (P<0.01) with the high concentrate diets. Chopping the forage decreased the concentration of fecal cellulolytic bacteria (P<0.05) but had no effect on their concentration in the rumen. An inverse linear relationship (P<0.01) was observed between total bacterial concentrations in the feces and diet intake. Although relationships were observed between the rumen and feces for total and cellulolytic bacterial concentrations, they were dependent on diet, particle size, and level of intake. Thus, fecal bacterial concentrations cannot be used to reliably predict rumen bacterial concentrations. Zoo Biol 27:100–108, 2008. © 2008 Wiley‐Liss, Inc.     

The effect of rumen ciliates on chitinolytic activity,chitin content and the number of fungal zoospores in the rumen fluid of sheep

The objective of this study was to investigate the effect of selected protozoa on the degradation and concentration of chitin and the numbers of fungal zoospores in the rumen fluid of sheep. Three adult ewes were fed a hay-concentrate diet, defaunated, then monofaunated with Entodinium caudatum or Diploplastron affine alone and refaunated with natural rumen fauna. The average density of the protozoa population varied from 6.1 · 10⁴ (D. affine) to 42.2 · 10⁴ cells/ml rumen fluid (natural rumen fauna). The inoculation of protozoa in the rumen of defaunated sheep increased the total activity of chitinolytic enzymes from 2.9 to 3.6 μmol N-acetylglucosamine/g dry matter (DM) of rumen fluid per min, the chitin concentration from 6.3 to 7.2 mg/g DM of rumen fluid and the number of fungal zoospores from 8.1 to 10.9 · 10⁵ cells/ml rumen fluid. All examined indices showed diurnal variations. Ciliate population density was highest immediately prior to feeding and lowest at 4 h thereafter. The opposite effects were observed for the numbers of fungal zoospores, the chitin concentration and chitinolytic activity. Furthermore, it was found that chitin from zoospores may account for up to 95% of total microbial chitin in the rumen fluid of sheep. In summary, the examined ciliate species showed the ability of chitin degradation as well as a positive influence on the development of the ruminal fungal population.     

Spatial and temporal variations of the bacterial community in the bovine digestive tract

Aims:  Improved knowledge of the bacterial community of the digestive tract is required to enhance the efficiency of digestion in herbivores. This work aimed to study spatial and temporal variations of the bacterial communities in the bovine digestive tract and their correlation with gut environmental parameters.
Methods and Results:  Rumen content and faeces of five cows were sampled for 3 weeks. In addition, reticulum content was sampled during the third week. Bacterial communities were assessed by studying capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. The bacterial community structure differed between the forestomach and faecal contents. The abundance of several operational taxonomic units changed from week to week. Bacterial community structure of the rumen was correlated to propionic acid and NH₃–N concentrations.
Conclusions:  The bacterial community of the bovine digestive tract varied in space and time.
Significance and Impact of the Study:  The study of the bacterial communities of the digestive tract in herbivores should be widened from the rumen to the large intestine. The amplitude and origin of the temporal variation of the ruminal bacterial community need to be better understood to improve the control of the fermentative activity in herbivores.