The effects of cleaning and disinfection in reducing Salmonella contamination in a laboratory model kitchen

AIMS: To establish a laboratory model to compare the effectiveness of detergent-based disinfection procedures for reducing cross-contamination risks during handling of contaminated chicken. METHODS AND RESULTS: During handling of chickens, artificially contaminated with Salmonella enteritidis PT4, the organism was widely spread to hands, cloths, and hand- and food-contact surfaces. Hygiene procedures were assessed on the basis of their ability to reduce the number of recoverable salmonellas to <1 CFU. Although detergent-based cleaning using a typical bowl-wash routine without rinsing produced some risk reduction (from 100 to 61.4% of contaminated surfaces), it was insufficient to consistently restore surfaces to a hygienic state. By combining detergent-based cleaning with a rinsing step or with hypochlorite at 500 ppm (of available chlorine) some further reduction in microbial risk was achieved, but was not considered satisfactory for food hygiene purposes. By contrast the risk reduction produced by hypochlorite at 5000 ppm was highly significant and was sufficient to reduce the number of contaminated surfaces to 2.9%. CONCLUSIONS: A key step in achieving a hygienic state through detergent-based cleaning is rinsing but even this will not produce a 'hygienic' result for difficult surfaces such as the chopping board or the dishcloth. Disinfectant compounds should be considered in order to reduce the potential for foodborne cross infection within the home environment. SIGNIFICANCE AND IMPACT OF THE STUDY: Although tests are available to determine the performance of disinfectants, there are no quantitative procedures available to compare the risk reduction achieved by disinfection with that produced by detergent-based procedures. This study describes a reproducible laboratory method which can be used to differentiate the effectiveness of different hygiene procedures for reducing cross-contamination risks during food handling.     

High diversity of tropical intertidal zone sponges in temperature, salinity and current extremes

The wide intertidal zone of the Quirimba Archipelago (Mozambique, East Africa) encompasses many different habitats, which all experience wide environmental variation. Large daily fluctuations in temperature occur when standing water is heated up at low tide to >10°C above ambient. Salinity may be high in the dry season and periodically almost fresh in the wet season. Very high current velocities (≈3 ms⁻¹) may occur and the direction of water flow is often complex. Sponges were a major component of the fauna (and dominate the sessile forms) in most of the eight habitats studied: exposed reef, sheltered reef, sand-rock, cave, reef boulders, boulders on sand, mangrove swamp and seagrass meadows. The highest number of sponge species occurred in the two reef habitats: from mean values of between ≈2.5 and ≈0.5 species/m² (upper and lower shore, respectively). The diversity of species present yielded a high Shannon index value of H=2.95 for the total of 33 species. A rank-abundance plot of the data showed a high level of equitability (J=0.84). Community similarity measurement using Bray–Curtis index showed two clusters; the exposed habitats of the reefs and sand-rock and the refugia of cave, reef and sand boulders.     

Bacterial diversity in the breadcrumb sponge Halichondria panicea (Pallas)

The aim of this study was to investigate the diversity and variability of bacterial communities associated with the marine sponge Halichondria panicea with respect to tissue compartmentalization as well as seasonal and small-scale geographic variation. Diversity of microorganisms in sponges was investigated recently, but work on the variability and succession of associated bacterial communities is rare. Despite some information on Pacific and Mediterranean sponges, it is still uncertain whether bacteria and sponges are specifically associated. In this study, H. panicea specimens were sampled throughout the year at different stations around the island of Helgoland (North Sea) and investigated using molecular tools. The bacterial community associated with H. panicea was diverse, consisting of one denaturing gradient gel electrophoresis (DGGE) band occurring in most 'tissue' samples and additional variable bands. Variability was observed between different sponge fractions (i.e. the aquiferous system and the 'tissue'), sampling locations, and sampling dates. A PCR-DGGE specific for the Roseobacter group of marine Alphaproteobacteria displayed low diversity and a marked similarity between all samples. Phylogenetic analysis also pointed to specific Alphaproteobacteria of the Roseobacter group, which was predominant in most sponge 'tissue' samples. We conclude that H. panicea harbour a specific Roseobacter population with varying bacterial co-populations occurring seasonally or on a small-scale geographically, sometimes even dominating the bacterial community.     

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.     

Reproductive processes in sponges: a critical evaluation of current data and views

The nature of a number of fundamental processes occurring during reproduction in sponges still remains in doubt. Among the more significant of these are: the true status of sponges described as dioecious, namely whether some are actually successive hermaphrodites; the origin of oogonia, which have recently been claimed to be derived from choanocytes; the origin and mechanism of formation of large spermatogenic masses; the specific pathway leading to fertilization taken by sperm cells within the sponge tissue of viviparous species; the role played during larval metamorphosis by somatic cells which are incorporated into embryos; the cell lineage of choanocytes which form flagellated chambers during larval metamorphosis; the specific relationship of somatic growth and dormancy to gametogenesis; the role of budding and fragmentation in population maintenance; the role, if any, of gemmules in dispersion. It is considered mandatory that new techniques be developed in order to further elucidate these and other reproductive processes and to gather definitive data concerning them. The employment of only microscopic techniques is ultimately insufficient for investigating the dynamic relationships of reproductive processes.     

Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges

Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.     

The putative functional ecology and distribution of archaeal communities in sponges,sediment and seawater in a coral reef environment

Archaea play crucial roles in a number of key ecological processes including nitrification and methanogenesis. Although several studies have been conducted on these organisms, the roles and dynamics of coral reef archaeal communities are still poorly understood, particularly in host and nonhost biotopes and in high (HMA) and low microbial abundance (LMA) sponges. Here, archaeal communities detected in six distinct biotopes, namely, sediment, seawater and four different sponge species Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus from the Spermonde Archipelago, SW Sulawesi, Indonesia were investigated using 454‐pyrosequencing of 16S rRNA genes (OTU cut‐off 97%). Archaeal communities from sediment and sponges were dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained almost 75% of the variation in archaeal composition, with clear separation between microbial assemblages from sediment, X. testudinaria and H. erectus (HMA). In contrast, samples from seawater and both Stylissa species (LMA) showed considerable overlap in the ordination and, furthermore, shared most abundant OTUs with the exception of a single dominant OTU specifically enriched in both Stylissa species. Predicted functional gene content in archaeal assemblages also revealed significant differences among biotopes. Different ammonia assimilation strategies were exhibited by the archaeal communities: X. testudinaria, H. erectus and sediment archaeal communities were enriched for glutamate dehydrogenase with mixed specificity (NAD(P)⁺) pathways, while archaeal planktonic communities were enriched for specific glutamate dehydrogenase (NADP⁺) and glutamate synthase pathways. Archaeal communities in Stylissa had intermediate levels of enrichment. Our results indicate that archaeal communities in different biotopes have distinct ecophysiological roles.     

Reproductive and recruitment dynamics of clionaid sponges on oyster reefs in North Carolina

Boring sponges belonging to the family Clionaidae have become a destructive nuisance to eastern oyster (Crassostrea virginica) aquaculture and restoration efforts in the southeastern USA. Clionaid sponges colonize the inner layers of oyster shells and remove carbonate material, compromising the quality and marketability of the oyster; however, relatively little is known about reproduction and recruitment of these sponges. Using histological techniques, reproductive activity of clionaid sponges was monitored at two sites (Cedar Island and Masonboro Sound) in coastal North Carolina. Sponge recruitment to limestone tiles (5×5 cm), oyster shells, and clam shells was monitored in 2013 and 2014; recruitment to the limestone tiles was statistically higher than recruitment to clam or oyster shells. Overall, seasonal patterns in reproduction and recruitment of clionaid sponges were generally similar at the two sites. Three species of clionaid sponge were found during field sampling (Cliona celata, C. lobata, and C. truitti), and reproductive activity (eggs and spermatocysts) of these species was observed from April to November, with peak reproduction occurring from June to September for C. lobata and from August to September for C. celata. Recruitment peaked in late summer/early fall. Additionally, the relationship between environmental conditions (temperature, salinity, dissolved oxygen, pH, and chlorophyll a) and clionaid recruitment was explored using a regression model. At Cedar Island, the best‐fit model included salinity and dissolved oxygen, while the best‐fit model at Masonboro Sound included temperature, pH, and salinity. The data from this study show that the primary reproduction and recruitment pulses occur in the fall for local clionaids, and thus mitigation strategies should be applied in the late fall or winter to minimize infestations.     

ADP-ribosyl cyclase and abscisic acid are involved in the seasonal growth and in post-traumatic tissue regeneration of Mediterranean sponges

In previous papers it has been demonstrated that the plant hormone abscisic acid (ABA) is responsible for the stimulation of water filtration and oxygen consumption elicited by a temperature increase in the Mediterranean demosponge Axinella polypoides. The signal transduction pathway triggered by ABA involves activation of ADP-ribosyl cyclase (ADPRC), leading to an increase of the intracellular concentration of cyclic ADP-ribose (cADPR), a universal and potent intracellular calcium mobilizer. These data prompted us to investigate the possible involvement of the ABA/ADPRC/cADPR system in the sponge life cycle and in post-traumatic tissue regeneration of Mediterranean sponges. ADPRC activity was detected in the cell lysate from several common Mediterranean sponge species, including Calcarea and Demospongiae. Specimens were collected monthly over a 2-year period, from January 2002 to April 2004. All species studied showed a peak of ADPRC activity during July and August 2003, concomitant with an anomalous heat wave that struck the whole Mediterranean basin during these months. In the aquarium, during spontaneous tissue regeneration, an increase of the [ABA]_i and of the ADPRC activity over time zero values was consistently observed. In conclusion, these results indicate that an increase of ABA content and of ADPRC activity correlates with the growth and with post-traumatic tissue regeneration in several Mediterranean sponge species, indicating that the ABA/ADPRC/cADPR system is involved in the response to environmental stress in sponges. Determination of ADPRC activity/ABA content may provide a means to assess metabolic activation of sponge populations under conditions of environmental stress.     

Cross-contamination in the kitchen: estimation of transfer rates for cutting boards, hands and knives

Aims: To quantify cross-contamination in the home from chicken to ready-to-eat salad. Methods and Results: Based on laboratory scenarios performed by de Jong et al. (2008) , transfer rates were estimated for Campylobacter jejuni and Lactobacillus casei as a tracer organism. This study showed that transfer characteristics for both micro-organisms were comparable when washing regimes and transfer via items (cutting board, hands and knives) were compared. Furthermore, the study showed that the use of separate transfer rates for transfer from chicken to items and from items to salad will lead to an overestimation of campylobacteriosis risk. Applying good hygienic practices resulted in final levels of bacteria in the salad below the detection limit. Our study showed that it is important to include these data points in model fitting. Conclusions: Results obtained in observational studies with Lact. casei can be translated to Camp. jejuni using the transfer rates obtained in this study. Cross-contamination by hands, cutting boards and knives was equally important. Significance and Impact of the Study: Cross-contamination should be incorporated in microbiological risk assessments. The present study contributes to this by quantifying transfer of Camp. jejuni and Lact. casei from raw chicken via various contact surfaces into the ready-to-eat product.     

Bacterial abundance and diversity in the Barbados Trench determined by phospholipid analysis

Abstract: The Barbados trench is characterized by large fields of volcanoes and mounds located over a distance of 30 km above the northern slope of a basement ridge corresponding to an inactive transform fault. Sediments from various locations were collected and analyzed for their lipid contents. Bacterial input to the overall biomass was estimated through the analysis of phospholipid ester-linked fatty acid (PLFA) profiles and glycerol ether lipids. Results indicated a eubacterial biomass estimated to be 10⁹cells (g dry wt)⁻¹. Individual fatty acid profiles revealed the presence of sulfur-oxidizing bacteria common to many deep-sea sites but also a large contribution of type I and type II methanotrophs to the eubacterial biomass. The presence of methanotrophs was further supported by the analysis of specific biomarkers of these microorganisms as well as some unusual trans fatty acid isomers. Anaerobic bacteria and presumbly sulfate reducing bacteria were also present, as well as archaebacteria and primarily methanogens, as indicated by glycerol ether lipid analysis.     

The distribution and prevalence of sponges in relation to environmental gradients within a temperate sea lough: vertical cliff surfaces

Abstract. The prevalence and distribution of sponges was surveyed on vertical cliff surfaces at Lough Hyne Marine Nature Reserve, Co. Cork, Ireland. The number of sponge species was recorded at 6-metre depth intervals at four sites within Lough Hyne, and at one site on the adjacent Atlantic coastline to examine differences in abundance and zonation patterns. Sites ranged from an exposed turbulent regime to sheltered, sedimented environments. Individual species showed different distributions and prevalence between sites and with increasing depth. Greatest differences were observed between the most- and least-disturbed sites. Distinct sponge zonation patterns were evident at all sites sampled. Twenty-five species were considered dominant at all five sites with the remaining 48 species considered rare. Only four of the 25 most-dominant species occurred at the site experiencing the most turbulent flow conditions, whereas 12 species were found at the site of unidirectional fast flow. At sites of moderate to slight water movement and high sedimentation, between 18 and 24 of the most dominant species were present. Encrusting forms constituted high proportions of sponge communities at all five sites sampled (although consisting of different species). At sites of turbulent and unidirectional fast flow massive forms also dominated whereas at the least turbulent sites, where sedimentation was high, arborescent sponges were abundant. Few species showed exclusive distribution to a single depth and site, but there was some degree of correlation between species distributions and abiotic factors such as sedimentation rate and flow regimes. Sponge distributions and densities are discussed with respect to the suitability of species' morphologies to particular environments, intra-specific and inter-specific competition and physiological adaptations that enable them to survive in different habitats.     

Effects of consumers and nitrogen availability on heterotrophic microbial activity during leaf decomposition in headwater streams

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The distribution and prevalence of sponges in relation to environmental gradients within a temperate sea lough: inclined cliff surfaces

Abstract. Sponge communities on inclined cliff surfaces (40°) at Lough Hyne Marine Nature Reserve, Co. Cork, Ireland were sampled at five sites (four inside the lough and one on the adjacent Atlantic coast). Each site varied in sedimentation rate and flow regime. Sites ranged from turbulent (with negligible sedimentation) to very low flow (< 3 cm⁻¹) and highly sedimented regimes. Sponge species showed variation between sites and depth. The greatest difference in sponge communities was observed between the most turbulent and most sedimented sites. The distinct zonation patterns, present at all sites, were most pronounced at the highly sedimented sites. Encrusting forms constituted a high proportion of the sponges at all sites. However encrusting species found at the turbulent site were different to those at the sedimented sites. Arborescent species were common, mainly at the sedimented sites within Lough Hyne. Distributions of sponge species are considered with respect to morphological adaptation, competition and physiological adaptation. The distributions of sponge species on inclined surfaces are also compared with those on vertical cliff faces.     

广西蚕沙细菌组成多样性解析和VBNC菌群的发掘

【目的】解析广西蚕沙中细菌群落组成与多样性,为蚕沙中菌种资源发掘和蚕沙的综合利用提供科学依据。【方法】通过高通量测序技术研究细菌群落组成特征,同时利用常规稀释涂布平板法和基于复苏促进因子(Rpf)的MPN培养系统解析并筛选蚕沙中可培养和活的非可培养(VBNC)状态的优势菌群,并经16SrRNA基因测序对筛选得到的菌株作初步分类鉴定。【结果】高通量测序表明,广西蚕沙样品中细菌归属于10个门、18个纲、27个目、57个科、96个属,其中4个属的丰度达1%以上,优势菌群为变形菌门(Proteobacteria)肠杆菌属(Enterobacter);通过稀释涂布平板法共获得14个属的33株可培养细菌,其中4个属(Citrobacter、Weissella、Chitinophaga、Pseudoclavibacter)在高通量测序中未被检测到;而在MPN培养系统中,基于复苏促进因子的处理组细菌总数最大检出丰度提高了100倍,并从中共检出21株对Rpf敏感的VBNC菌株,其中6个属(Paenibacillus、Caulobacter、Roseomonas、Pantoea、Erwinia、Acine...     

基于高通量测序的黄河三角洲4种人工林土壤细菌结构及多样性研究

为研究黄河三角洲不同人工林土壤细菌群落特征,应用高通量测序技术,比较分析了刺槐、榆树、白蜡、臭椿4种人工林土壤细菌结构及多样性,并结合土壤理化性质进行相关性分析。结果表明:人工林土壤中共有31门细菌;4种人工林土壤中酸杆菌门、变形菌门、放线菌门细菌以及刺槐、臭椿人工林土壤中硝化螺旋菌门细菌是土壤中的优势群落。不同人工林土壤中酸杆菌门、变形菌门、硝化螺旋菌门、芽单胞菌门、拟杆菌门、广古菌门、泉古菌门、蓝藻菌门细菌丰度差异显著。刺槐人工林土壤细菌多样性最高;白蜡人工林土壤细菌多样性最低。土壤pH、含水量、有机质含量与酸杆菌门细菌丰度呈显著负相关关系,土壤pH与变形菌门、硝化螺旋菌门、芽单胞菌门细菌丰度呈极显著正相关关系;土壤pH、有效磷含量与人工林细菌多样性呈显著正相关关系。以上研究结果表明,黄河三角洲不同人工林土壤细菌群落存在一定差异,土壤pH、含水量、有机质、有效磷含量是影响土壤细菌结构和多样性的主要土壤因素。     

Bacterial diversity in Greenlandic soils as affected by potato cropping and inorganic versus organic fertilization

Arctic and Subarctic ecosystems will in the near future be exposed to severe environmental stresses due to global warming. For example, the microbial community structure and function may change as a result of increased temperatures. In Greenland, agriculture is carried out in the Subarctic regions with only limited pest management, despite the presence of plant pathogenic fungi. The microbial community composition in agricultural soils, which plays an important role for soil and plant health and for crop yield, may be affected by the use of different fertilizer treatments. Currently, only limited research has been performed on the effects of these treatments on bacterial communities in Arctic and Subarctic agricultural soils. The major objective of this study was to investigate the short-term impact of conventional (NPK) and organic (sheep manure supplemented with nitrogen) fertilizer treatments on bacterial diversity, nutrient composition and crop yield in two Greenlandic agricultural soils. An effect of fertilizer was found on soil and plant nutrient levels and on crop yields. Pyrosequencing of 16S rRNA gene sequences did not reveal any major changes in the overall bacterial community composition as a result of different fertilizer treatments, indicating a robust microbial community in these soils. In addition, differences in nutrient levels, crop yields and bacterial abundances were found between the two field sites and the two experimental growth seasons, which likely reflect differences in physical–chemical soil parameters.     

Culture-independent nested PCR method reveals high diversity of actinobacteria associated with the marine sponges <Emphasis Type="Italic">Hymeniacidon perleve</Emphasis> and <Emphasis Type="Italic">Sponge</Emphasis> sp.

A culture-independent nested polymerase chain reaction (PCR) technique was used to investigate the diversity of actinobacteria communities associated with the sponges Hymeniacidon perleve and Sponge sp. The phylogenetic affiliation of sponge-derived actinobacteria was then assessed by 16S rRNA sequencing of cloned DNA fragments. A total of 196 positive clones were screened by restriction fragment length polymorphism (RFLP) analysis; 48 unique operational taxonomic units (OTUs) were selected for sequencing. Rarefaction analysis indicated that the clone libraries represented 93% and 94% of the total estimated diversity for the two species, respectively. Phylogenetic analysis of sequence data revealed representatives of various phylogenetic divisions, which were related to the following ten actinobacterial genera: Acidimicrobium, Corynebacterium, Propionibacterium, Actinomyces, Micrococcus, Microbacterium, Streptomyces, Mycobacterium, Cellulosimicrobium, Sporichthya, and unidentified actinobacterial clones. A sponge-specific, previously uncultured actinobacteria community grouped within the subclass Acidimicrobidae was discovered from both H. perleve and Sponge sp. Sequences belonging to Acidimicrobium in the H. perleve and the Sponge sp. clone libraries represented 33% and 24% of the clones, respectively. In the Sponge sp. clone library Mycobacterium dominated, accounting for 70% of all clones. The presence of Acidimicrobium and mycobacteria within two sponges can lay the groundwork for attempts to culture these interesting bacteria for industrial applications.