Spatial and temporal variations in fish populations in the upper Thames estuary

Between February 1989 and August 1990, the upper Thames estuary contained 23 species of fish. Fish numbers were higher and relatively constant in the uppermost part of the estuary. Number of species was augmented in summer from fresh water and from downstream, coinciding with high temperature, low flow and high salinity. The eight most abundant species contributed to 98·5% of the total number. Flounder Pleuronectes flesus , dace Leuciscus leuciscus and perch Perca fluviatilis , recruited from May to August, and common goby Pomatoschistus microps , roach Rutilus rutilus and chub Leuciscus cephalus , from August to November. The upper estuary (salinity 0·34–2·96 p.s.u.) formed a species transition area between the freshwater but salinity-resistant roach, chub, and gudgeon Gobio gobio upstream, and the estuarine eurhyhaline common goby and flounder downstream. The three-spined stickleback Gasterosteus aculeatus and cyprinids were more abundant at upstream while perch was more abundant at downstream sites. High abundances of gudgeon, chub and roach were associated with high transparency and dissolved oxygen and low salinity, while high abundances of perch were associated with high salinity and low transparency. Dace and three-spined stickleback were associated with high dissolved oxygen and low pH, and common goby with high pH. Flounder showed no clear preferences.     

Rapid adaptation of the bacterial community in the growing rabbit caecum after a change in dietary fibre supply

This work aimed to study the response of the growing rabbit caecal ecosystem (bacterial community and caecal environmental parameters) after a switch from a control to a low-fibre diet (LFD). A group of 160 rabbits were fed ad libitum a control diet (ADF: 20.4%) from weaning (36 days). At 49 days of age (day 0), 75 rabbits were switched to a LFD group (ADF: 10.7%), whereas 85 others (control group) remained on the control diet, for 39 days. Caecal contents were regularly sampled throughout the trial (60 rabbits per group). The bacterial community structure was characterized using CE-SSCP (capillary electrophoresis single strand conformation polymorphism) and total bacteria were quantified using real-time PCR. Redox potential (Eh), pH, NH(3)-N, volatile fatty acid (VFA) were measured in the caecum to characterize environmental parameters. The reduction of fibre in the diet modified the CE-SSCP profiles (P < 0.001) but not the diversity index (5.6 ± 0.8, ns). The number of 16S rRNA gene copies of total bacteria decreased (P < 0.01) in LFD rabbits compared with controls. In LFD rabbits, the caecal environment was less acid (+0.2 units; P < 0.01), more reductive (-11 mV; P < 0.05) and drier (+3.4 g 100 per g; P < 0.001), with an increase in NH3-N (+77%; P < 0.001) and a decrease in total VFA concentration (-17%; P < 0.001). We found significant correlations between the bacterial community, the quantity of bacteria and the caecal traits of the caecal ecosystem. Indeed, in both groups, the caecal traits barely constrained the total inertia of the CE-SSCP profile set (less than 14%), whereas total bacteria were positively related to total VFA, acetic acid and butyric acid levels, and Eh, and negatively related to pH. All the microbial and environmental modifications had occurred by day 2 and remained stable thereafter. These results suggest that the bacterial community in the growing rabbit caecum is able to adapt quickly after a change to in the dietary fibre supply to reach a new steady-state equilibrium.     

Molecular analysis of the bacterial community in digestive tract of rabbit

This work aimed to study the stability over time of the bacterial community in cæcum and fæces of the rabbit (diversity index and structure) without experimental disturbance and to evaluate its relationships with environmental parameters. Soft and hard fæces of 14 rabbits were sampled for 5 weeks while cæcal content was sampled on the 3rd week (by surgery) and the 5th week (at slaughter). Bacterial communities were assessed by studying CE-SSCP profiles of 16S rRNA genes fragments. Redox potential, pH, NH3-N concentration and volatile fatty acid concentrations were measured in the cæcum. Data showed that bacterial communities of soft and hard fæces barely differed from that of the cæcum (ANOSIM-R < 0.25; p < 0.05). Without disturbance, the bacterial communities of fæces were stable over time (ANOSIM-R < 0.25; p < 0.001). However, the bacterial communities of cæcum and fæces were affected by the surgery (ANOSIM-R = 0.22–0.33; p < 0.001). The cæcal content was an acidic (pH = 6.03 ± 0.33) and an anaerobic environment (redox potential = ?160 ± 43 mV). Only the redox potential was correlated with the diversity index of the bacterial community of the cæcum (R² = 0.35; p < 0.05) and no environmental parameters were correlated to its structure.     

Exploring the bovine rumen bacterial community from birth to adulthood

The mammalian gut microbiota is essential in shaping many of its host''s functional attributes. One such microbiota resides in the bovine digestive tract in a compartment termed as the rumen. The rumen microbiota is necessary for the proper physiological development of the rumen and for the animal''s ability to digest and convert plant mass into food products, making it highly significant to humans. The establishment of this microbial population and the changes occurring with the host''s age are important for understanding this key microbial community. Despite its importance, little information about colonization of the microbial populations in newborn animals, and the gradual changes occurring thereafter, exists. Here, we characterized the overall bovine ruminal bacterial populations of five age groups, from 1-day-old calves to 2-year-old cows. We describe the changes occurring in the rumen ecosystem after birth, reflected by a decline in aerobic and facultative anaerobic taxa and an increase in anaerobic ones. Some rumen bacteria that are essential for mature rumen function could be detected as early as 1 day after birth, long before the rumen is active or even before ingestion of plant material occurs. The diversity and within-group similarity increased with age, suggesting a more diverse but homogeneous and specific mature community, compared with the more heterogeneous and less diverse primary community. In addition, a convergence toward a mature bacterial arrangement with age was observed. These findings have also been reported for human gut microbiota, suggesting that similar forces drive the establishment of gut microbiotas in these two distinct mammalian digestive systems.     

Spatial and temporal population dynamics of a naturally occurring two-species microbial community inside the digestive tract of the medicinal leech

The medicinal leech, Hirudo verbana, is one of the simplest naturally occurring models for digestive-tract symbioses, where only two bacterial species, Aeromonas veronii bv. sobria (gamma-Proteobacteria) and a Rikenella-like bacterium (Bacteroidetes), colonize the crop, the largest compartment of the leech digestive tract. In this study, we investigated spatial and temporal changes of the localization and microcolony structure of the native symbionts in the crop, after ingestion of a sterile blood meal, by fluorescence in situ hybridization. The population dynamics differed between the two symbiotic bacteria. A. veronii was detected mainly as individual cells inside the intraluminal fluid (ILF) during 14 days after feeding (daf) unless it was found in association with Rikenella microcolonies. The Rikenella-like bacteria were observed not only inside the ILF but also in association with the luminal surface of the crop epithelium. The sizes of Rikenella microcolonies changed dynamically through the 14-day period. From 3 daf onward, mixed microcolonies containing both species were frequently observed, with cells of both species tightly associating with each other. The sizes of the mixed microcolonies were consistently larger than the size of either single-species microcolony, suggesting a synergistic interaction of the symbionts. Lectin staining with succinylated wheat germ agglutinin revealed that the planktonic microcolonies present in the ILF were embedded in a polysaccharide matrix containing N-acetylglucosamine. The simplicity, symbiont-symbiont interaction, and mixed microcolonies of this naturally occurring, digestive-tract symbiosis lay the foundation for understanding the more complex communities residing in most animals.     

The prevalence of Salmonella spp. in bovine faecal,rumen and carcass samples at a commercial abattoir

AIMS: To determine the prevalence, serotype and antibiotic resistance profile of Salmonella isolates in cattle and on carcasses at a commercial Irish abattoir. METHODS AND RESULTS: Faecal, rumen and carcass samples were collected from a beef abattoir over a 12-month period and examined for the presence of Salmonella spp. Isolates were serotyped, phage typed (when serotype was found to be S. Typhimurium) and tested for susceptibility to a panel of antibiotics. Salmonella was isolated from 2% of faecal, 2% of rumen and 7.6% of carcass samples. Salmonella was most frequently isolated from samples taken during the period August to October. S. Dublin was isolated from 72% of positive samples. S. Agona and S. Typhimurium definitive type (DT)104 were each isolated from 14% of positive samples. All S. Typhimurium DT104 isolates were resistant to ampicillin, chloramphenicol, streptomycin, sulphafurazole and tetracycline (ACSSuT). On occasion, from a single animal, the same serotype was isolated from more than one sample (i.e. faeces and rumen; faeces and carcass; rumen and carcass; faeces, rumen and carcass). CONCLUSIONS: Salmonella is present in cattle at slaughter and on beef carcasses at an Irish abattoir, with a higher frequency of occurrence during the period August to October. Most isolates from the study are not commonly associated with human clinical infection, with the exception of S. Typhimurium DT104 (R-type ACSSuT). SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides epidemiological data that is necessary for the understanding of beef as a source of human Salmonella infection.     

Spatial and temporal variability of antibiotic resistance in freshwater bacterial assemblages

Abstract Spatial and temporal variability in antibiotic resistance was examined in bacterial assemblages from streams and ponds on the US Department of Energy's Savannah River Site (SRS) in South Carolina. Sites sampled have been impacted to varying degrees by contamination with organic compounds, heavy metals, and radioactive materials because of production of nuclear materials on the site. Antibiotic resistance in the culturable portion of the bacterial assemblage was determined from coloby formation on media containing antibiotics. Eight antibiotics, chloramphenicol, cycloserine, kanamycin, neomycin, novobiocin, rifampicin, streptomycin, and tetracycline, were used at concentrations of 50 and 200 μg ml⁻¹. Statistically significant differences in frequency of antibiotic resistance were observed among sites and among dates at a single site. Bacterial densities (total and culturable), dissolved organic carbon (DOC) concentration, and human impact also varied among sites but bore no overall relationship to resistance frequency. SRS operations did not have a detectable impact on antibiotic resistance.     

Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen

Microbial colonization is central to ruminal degradation of dietary material yet little is known about the dynamics of this process. The aim of this study was to characterize the initial stages of bacterial colonization of forage, and to assess the impact that different postsample processing and analysis methods had on the results obtained. Bacterial 16S rRNA gene-based analysis of damaged, nonconserved perennial ryegrass, incubated in sacco in the bovine rumen, required the development and validation of new quantitative PCR and denaturing gradient gel electrophoresis (DGGE) primers. Analysis with previously available primer sets was compromised due to dominant amplification of forage-derived chloroplast 16S rRNA genes. DGGE analysis of incubated samples demonstrated that a diverse and consistent population of ruminal bacteria colonized rapidly. Postsampling methodologies did not affect overall population profiles whereas the washing method appeared to influence bacterial numbers. However, regardless of processing methodology, bacterial numbers increased rapidly within 5 min, stabilizing after 15 min of incubation. These findings reveal for the first time the dynamics of bacterial colonization of forage within the rumen.     

Effects of sampling location and time,and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen

Aims: To investigate, using culture‐independent methods, whether the ruminal bacterial structure, population and fermentation parameters differed between sampling locations and time. Methods and Results: The detectable bacteria and fermentation parameters in the digesta from five locations in the rumen of three cows at three time points were analysed. The PCR‐denaturing gradient gel electrophoresis (PCR‐DGGE) profiles were similar among digesta samples from five locations (95·4%) and three time points (93·4%) within cows; however, a lower similarity was observed for samples collected from different host animals (85·5%). Rumen pH and concentration of volatile fatty acids (VFA) were affected by time points of sampling relative to feeding. Conclusions: The detectable bacterial structure in the rumen is highly conserved among different locations and over time, while the quantity of individual bacterial species may change diurnally in response to the feeding. Significance and impact of the study: This study supplies the fundamental understanding of the microbial ecology in the rumen, which is essential for manipulation of ruminal microflora and subsequent improvement in animal production.     

Carbohydrase activities in the bovine digestive tract

1. The carbohydrase activities of homogenates of mucosa from the abomasum, small intestine, caecum and colon, and of the pancreas of cattle were studied. 2. The disaccharidase activities were located mainly in the small intestine and showed a non-uniform pattern of distribution along the small intestine; trehalase activity was highest in the proximal part, lactase and cellobiase activities were highest in the proximal and middle parts and maltase activity was highest in the distal part. 3. The intestinal lactase and cellobiase activities were highest in the young calf and decreased with age, whereas the intestinal maltase and trehalase activities, which were very low compared with the lactase activity, did not change with age. 4. No intestinal sucrase or palatinase activity was detected in the calf or in the adult cow. 5. Homogenates of intestinal mucosa also exhibited amylase and dextranase activity. 6. Homogenates of the pancreas possessed a strong amylase activity and a weak maltase activity. The maltase activity did not change with age, whereas the amylase activity increased with age. 7. No marked differences were observed between the carbohydrase activities of calves fed solely on milk and those of calves given a concentrate-hay diet from 6 weeks of age.     

Effects of varying proportions of concentrates on ruminal-reducing power and bacterial community structure in dry dairy cows fed hay-based diets

The objectives of this study were to evaluate the influence of diet composition on ruminal parameters, more particularly redox potential (Eh). Four Holstein dry dairy cows, fitted with ruminal cannulas, were allocated in a 4 × 4 Latin square design. They were given four experimental hay-based diets D0, D25, D42 and D56 consisting of 0%, 25%, 42% and 56% of ground wheat and barley concentrate mixture, respectively. They were fed at a daily feeding rate of 8.0 kg DM per cow during a 24-day experimental period (a 21-day diet adaptation, three consecutive days of measurement and sampling). The physicochemical parameters, such as pH and Eh, were measured and Clark's exponent (rH) was calculated from 1 h before feeding to 8 h after feeding at 1-h interval. Samples of ruminal fluid were taken at 0, 1, 2, 4, 6 and 8 h after feeding for the determination of volatile fatty acid (VFA) and ammonia N (NH3-N) concentrations. Ruminal bacterial populations were also studied by means of capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) technique to focus on the structure of the ruminal microbiota and the diversity index was calculated. Mean ruminal Eh and rH were not modified by the concentrate-to-forage ratio and averaged - 210 mV and 6.30, respectively, across diets. The pH decreased slightly by 0.10 pH unit between treatments D0 and D56 with an average of 6.58. Nevertheless, the time during which physicochemical parameters remained at nadir value after feeding varied with diets: 2 and 7 h for D0 and 6 and 5 h for D56, respectively for pH and Eh. Moreover, fermentative parameters were altered by treatments: total VFA and NH3-N were greater in D56 (72.2 mM and 17.5 mg/100 ml) compared with D0 (65.2 mM and 14.2 mg/100 ml). However, neither the structure of bacterial populations of the rumen nor the diversity index (Shannon) was altered by treatments.     

长江口及其邻近海域春季无脊椎动物群落时空变化

为了研究长江口及其邻近海域无脊椎动物群落结构和多样性的时空变化特征, 我们于1999-2012年春季在长江口及其邻近海域采用定点底层双拖网调查方式进行无脊椎动物调查。结果表明: (1)1999-2012年长江口水域共记录无脊椎动物41种, 隶属6纲10目23科, 其中甲壳动物种类最多(26种), 其次为软体动物(13种)。不同年份种类数量呈先下降后上升的趋势。(2)优势种主要包括日本枪乌贼(Loligo japonica)、三疣梭子蟹(Portunus trituberculatus)、葛氏长臂虾(Palaemon gravieri)和鹰爪虾(Trachypenaeus curvirostris)等, 其在年间存在剧烈变动, 但日本枪乌贼几乎每年都是优势种。(3)长江口无脊椎动物丰度、种类丰富度和多样性在年间均存在显著差异, 1999年和2001年最高, 2004年后呈先下降后恢复上升的趋势。(4)长江口水域的无脊椎动物在每个航次调查中都存在2-3个群聚类型, 并有不同的指示种类。(5)1999-2012年长江口无脊椎动物群落的时间变化可划分为3个阶段: 1999-2001年多样性程度最高, 2004-2007年下降至最低水平, 2009-2012年多样性显著回升, 但尚未恢复到1999-2001年的水平。与20世纪80年代相比, 蟹类减少导致长江口无脊椎动物生物量整体水平下降, 高营养级生物资源衰退带来了无脊椎动物中低营养级生物种群的迅速发展。     

Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea

The structure of the total and metabolically active communities of attached and free-living bacteria were analysed in the euphotic zone in the NW Mediterranean Sea with the use of DNA- and RNA-derived capillary electrophoresis single-strand conformation polymorphism fingerprinting. More than half (between 52% and 69%) of the DNA-derived operational taxonomic units (OTUs) were common in both attached and free-living fractions in the euphotic layer, suggesting an exchange or co-occurrence between them. However, analysis targeting 16S rRNA showed that only some of them were found in the dominant active bacterial pool. Especially at the deep chlorophyll maximum, less than half of the attached bacterial populations were found to be active, with regard to the high proportion of OTUs present at the DNA level, but not at the RNA level. These results suggest that even if colonization on and detachment of particles appear to be ubiquitous, most of the particulate organic carbon remineralization appeared to be mediated by a rather low number of dominant active OTUs specialized in exploiting such specific microenvironment.     

Spatial and temporal variations in chitinolytic gene expression and bacterial biomass production during chitin degradation

Growth of the chitin-degrading marine bacterium S91 on solid surfaces under oligotrophic conditions was accompanied by the displacement of a large fraction of the surface-derived bacterial production into the flowing bulk aqueous phase, irrespective of the value of the surface as a nutrient source. Over a 200-h period of surface colonization, 97 and 75% of the bacterial biomass generated on biodegradable chitin and a nonnutritional silicon surface, respectively, detached to become part of the free-living population in the bulk aqueous phase. Specific surface-associated growth rates that included the cells that subsequently detached from the substrata varied depending on the nutritional value of the substratum and during the period of surface colonization. Specific growth rates of 3.79 and 2.83 day(-1) were obtained when cells first began to proliferate on a pure chitin film and a silicon surface, respectively. Later, when cell densities on the surface and detached cells as CFU in the bulk aqueous phase achieved a quasi-steady state, specific growth rates decreased to 1.08 and 0.79 day(-1) on the chitin and silicon surfaces, respectively. Virtually all of the cells that detached from either the chitin or the silicon surfaces and the majority of cells associated with the chitin surface over the 200-h period of surface colonization displayed no detectable expression of the chitin-degrading genes chiA and chiB. Cells displaying high levels of chiA-chiB expression were detected only on the chitin surface and then only clustered in discrete areas of the surface. Surface-associated, differential gene expression and displacement of bacterial production from surfaces represent adaptations at the population level that promote efficient utilization of limited resources and dispersal of progeny to maximize access to new sources of energy and maintenance of the population.     

牛瘤胃分离菌株静息细胞培养体系生物转化黄豆苷原

从牛瘤胃胃液中分离了一株在厌氧条件下能利用其生长细胞将大豆异黄酮黄豆苷原高效还原为二氢黄豆苷原的革兰氏阳性细菌菌株Niu-O16。研究了菌株Niu-O16静息细胞体系转化黄豆苷原的最佳转化条件,通过单因素试验确定菌株Niu-O16静息细胞转化黄豆苷原的最佳条件是:初始pH6.0～8.0,静息细胞浓度32～64mg/mL(湿重),加入底物浓度0.8～1.2mmol/L。通过正交试验确定了静息细胞浓度、加入底物浓度及转化时间的最佳组合为:静息细胞浓度32mg/mL、加入底物浓度0.8mmol/L、转化时间24h;最佳转化条件下底物转化率最高为63.9%。该结果为厌氧菌的静息细胞转化及工业应用提供了参考。     

A survey of enteric bacteria and protozoans in fresh bovine faeces on New Zealand dairy farms

Aims: To determine the counts and/or prevalence in fresh bovine faeces of Escherichia coli, enterococci, Campylobacter, Salmonella, shiga toxin‐producing E. coli (STEC), Giardia and Cryptosporidium, as inputs to numerical models designed to estimate microbial loadings on pasture grazed by cattle in New Zealand. Methods and Results: In each season over one year, samples of freshly deposited bovine faeces were collected from four New Zealand dairy farms (n = 155), and enumerated for E. coli, enterococci, Campylobacter, Giardia and Cryptosporidium. They were also tested for the presence of Salmonella and STEC. The overall median bacterial counts (g^?1 wet weight) were E. coli– 5·9 × 10⁶; enterococci – 1·3 × 10⁴; Campylobacter– 3·9 × 10⁵. All counts were highly variable within and between samplings, and few seasonal or regional patterns emerged. However, mean Campylobacter counts were consistently higher in spring. No Salmonella spp. was detected, and only two samples were positive for STEC. Cryptosporidium and Giardia were isolated from 5·2% and 4·5% of the samples, respectively, yielding low numbers of (oo)cysts (1–25 g^?1 and 1–17 g^?1, respectively). Conclusions: Fresh bovine faeces are a significant source of E. coli, enterococci and Campylobacter on New Zealand pastures, although numbers are likely to vary markedly between faecal samples. Significance and Impact of the Study: The study provides the first significant set of indicator and pathogen counts for one of the largest sources of faecal contamination of natural waters in New Zealand, and will be used to model these inputs.     

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.     

Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth

The objective of this study was to determine whether host, compartment, or environmental specific factors play an important role in the establishment of the intestinal microflora in broiler chickens during growth. This objective was addressed using a 16S rDNA approach. PCR-amplicons from the V6 to V8 regions of the 16S rDNA of intestinal samples were separated by denaturing gradient gel electrophoresis (DGGE). The number of bands in all intestinal compartments increased when broilers grew older, indicating that the dominant bacterial community becomes more complex when chickens age. Each chicken had a unique banding pattern for all locations in the intestinal tract, irrespective of the age of chickens. This suggests that host-related factors affect the establishment of the dominant bacterial community. Banding patterns of intestinal compartments within one chicken were different from each other for broilers older than 4 days, except for both ceca which were highly similar. In 4-day-old broilers, banding patterns from crop, duodenum, and ileum were very similar. We conclude that (unknown) host specific factors play an important role in the development of the intestinal bacterial community in each broiler chicken. Furthermore, compartment-specific factors play an important role in the bacterial development of each intestinal compartment within one chicken.