Evaluation of three newly developed direct plating media to enumerate Listeria monocytogenes in foods

LiCl-phenylethanol-moxalactam Agar (LPMA), ARS Modified McBride Agar, and Modified Vogel Johnson Agar were compared with previously tested plating media in the enumeration of Listeria monocytogenes from pasteurized whole milk, chocolate ice cream mix, Brie cheese, and raw cabbage. LPMA was most suitable for analyzing Brie cheese and cabbage. Gum base-nalidixic acid-tryptone-soya medium (previously tested) was most suitable for analyzing milk and chocolate ice cream mix.     

Evaluation of three newly developed direct plating media to enumerate Listeria monocytogenes in foods.

LiCl-phenylethanol-moxalactam Agar (LPMA), ARS Modified McBride Agar, and Modified Vogel Johnson Agar were compared with previously tested plating media in the enumeration of Listeria monocytogenes from pasteurized whole milk, chocolate ice cream mix, Brie cheese, and raw cabbage. LPMA was most suitable for analyzing Brie cheese and cabbage. Gum base-nalidixic acid-tryptone-soya medium (previously tested) was most suitable for analyzing milk and chocolate ice cream mix.     

Ecotonal shifts in diversity and functional traits in zoobenthic communities of karst springs

We examined the potential importance of distance from the spring source (reach), season, and physicochemical variability on zoobenthic biodiversity, biomass, and trait-based metrics [functional feeding groups (FFG) and habit traits] in three karst spring systems in the Ozarks region of Missouri, USA. Density and biomass were measured during summer and winter in each spring source and three downstream reaches of each springbrook. Nearly 20,000 invertebrates in total were collected, identified, and counted. We measured biomass directly or by length–weight relationships. Overall downstream and seasonal patterns of diversity, biomass, and traits were similar among springs, but species dominance and composition varied significantly. Taxonomic richness increased downstream in all springs, but evenness decreased. Amphipods and isopods were the most abundant taxa at the spring source but were progressively replaced downstream by insects (with dominance varying among springs and seasons). Density and biomass for flatworms, snails, and insects increased downstream, while crustacean numbers diminished along this ecotone. FFG increased from 3 at the spring source (mostly shredders) to 4–7 downstream where scrapers, collectors, and/or predators predominated. Physicochemical factors proved minor at best as mechanistic explanations for ecotonal changes. We conclude that structural and functional community changes could be attributed to a matrix of interrelated factors including organic substrate, food availability, and biotic interactions.     

Enrichment of anaerobic heterotrophic thermophiles from four Azorean hot springs revealed different community composition and genera abundances using recalcitrant substrates

DGGE analysis combined with a metagenomic approach was used to get insights into heterotrophic anoxic enrichment cultures of four hot springs of Vale das Furnas, Portugal, using the recalcitrant substrate spent coffee ground (SCG). Parallel enrichment cultures were performed using the major components of spent coffee ground, namely arabinogalactan, galactomannan, cellulose, and proteins. DGGE revealed that heterotrophic thermophilic bacteria are highly abundant in the hydrothermal springs and significant differences in community composition depending on the substrate were observed. DNA, isolated from enrichment cultures of different locations that were grown on the same substrate were pooled, and the respective metagenomes were analyzed. Results indicated that cultures grown on recalcitrant substrate SCG consists of a totally different thermophilic community, dominated by Dictyoglomus. Enrichments with galactomannan and arabinogalactan were dominated by Thermodesulfovibrio, while cultures with casein and cellulose were dominated by Thermus. This study indicates the high potential of thermophilic bacteria degrading recalcitrant substrate such as SCG and furthermore how the accessibility to complex polymers shapes the bacterial community.

     

Identification of nitrogen sources and transformations within karst springs using isotope tracers of nitrogen

Isotope analyses of nitrate and algae were used to gain better understanding of sources of nitrate to Florida’s karst springs and processes affecting nitrate in the Floridan aquifer at multiple scales. In wet years, δ¹⁵N and δ¹⁸O of nitrate ranged from +3 to +9‰ in headwater springs in north Florida, indicating nitrification of soil ammonium as the dominant source. With below normal rainfall, the δ¹⁵N and δ¹⁸O of nitrate were higher in almost all springs (reaching +20.2 and +15.3‰, respectively) and were negatively correlated with dissolved oxygen. In springs with values of δ¹⁵N-NO₃ and δ¹⁸O-NO₃ greater than +10‰, nitrate concentrations declined 40–50% in dry years and variations in the δ¹⁵N and δ¹⁸O of nitrate were consistent with the effects of denitrification. Modeling of the aquifer as a closed system yielded in situ fractionation caused by denitrification of 9 and 18‰ for Δ¹⁸O and Δ¹⁵N, respectively. We observed no strong evidence for local sources of nitrate along spring runs; concentrations declined downstream (0.42–3.3?μmol-NO₃ L^?1 per km) and the isotopic dynamics of algae and nitrate indicated a closed system. Correlation between the δ¹⁵N composition of nitrate and algae was observed at regional and spring-run scales, but the relationship was complicated by varying isotopic fractionation factors associated with nitrate uptake (Δ ranged from 2 to 13‰). Our study demonstrates that nitrate inputs to Florida’s springs are derived predominantly from non-point sources and that denitrification is detectable in aquifer waters with relatively long residence time (i.e., matrix flow).     

Evaluation of techniques to detach particle-associated microorganisms from rumen contents

Effects of the most commonly used treatments to detach particle-associated microorganisms from rumen contents were investigated using rumen particles of different sizes. Particles were obtained before feeding from ruminally cannulated sheep. The extent of microorganism dissociation was determined using ¹⁵N as an external marker. The first experiment studied the effect of anaerobiosis on efficiency of 1 g/l methylcellulose, pH 8, and chilling (4 °C). Due to poor detachment, the anaerobic procedure was discarded. The following factors, separately or in combination, were then examined in aerobic conditions on two classes of particles obtained from whole ruminal contents (large: >400 μm; small: 100–400 μm) being: (a) stomacher pummelling (5 min); (b) Waring blender homogenisation (3×1 min); (c) chilling (4 °C); (d) pH 8; (e) 1 g/l methylcellulose; (f) 10 ml/l methanol and 10 ml/l tertiary butanol. Samples were incubated for 5 h, except for treatments (a) and (b), and washed after treatment for 2 min under running tap water in a 25 μm gauze. Blending proved to be the most effective treatment (from 50 to 57% removal). Combinations of treatments did not improve detachment. N losses from treated samples were linearly related to ¹⁵N removal. The percentage of particles removed was calculated using incubated and/or washed particles as the control, according to treatments. Results suggest that caution is needed when evaluating the effectiveness of treatments, because results are dependent on the type of particles chosen as the control.     

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes

The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ~4% read abundance across biological, and ~2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific 'in vivo' fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.     

Mediterranean karst springs: diatom biodiversity hotspots under the pressure of hydrological fluctuation and nutrient enrichment

Abstract

Mediterranean karst springs are affected by strong climatic seasonality, with long, dry and hot summers and are increasingly threatened by anthropogenic pressures. In Sardinia (western Mediterranean Sea, Italy), they are largely unexplored and their biocoenoses are mostly unknown. The diatom flora from two substrates (cobbles and macrophytes) in eight springs of different areas of the island was investigated in summer 2016 and winter 2017. A total of 162 diatom taxa (58 genera) were found of which 27 (17 genera) only on cobbles and 26 (18 genera) only on macrophytes. The most abundant species from both substrates were Achnanthidium minutissimum, Amphora indistincta, Amphora pediculus, Cocconeis euglypta, Planothidium frequentissimum and P. lanceolatum. Overall, 67 taxa (40 genera) were recorded in single sites and some of these taxa showed high affinity with specific environmental conditions. Hydrological stability (water flow permanence), discharge and nutrients were the main environmental factors influencing diatom assemblages. Our results suggest that diatoms can reflect important local factors related to the vulnerability of these spring ecosystems and underline the importance of their preservation both for biodiversity and water quality maintenance.     

我国北方岩溶泉域刚毛藻的系统发育及形态学研究

脆弱刚毛藻(Cladophora fracta)是一种大型丝状绿藻,生境分布广泛。然而,对于岩溶泉域分布的刚毛藻研究较少,它们的遗传多样性、生物地理亲缘性和生理特性都有待于深入研究。该研究对我国北方地区五个典型岩溶泉域的50个脆弱刚毛藻样本进行了形态学和分子系统学描述。主要研究目标:(1)对我国北方地区五个典型岩溶泉的刚毛藻生境进行描述;(2)根据形态学特征和分子序列对藻体进行鉴定;(3)探究生境对藻体生理特性的影响。结果表明:基于SSU和LSU序列的结果,发现所分析的50株刚毛藻个体为同一种,同时还发现了13个不同的核糖体基因型。基于SSU和LSU的系统发育树,刚毛藻属均未能形成单系分支,分布在三个不同的分支上。13个样本基因型在SSU和LSU树中的位置相似,与Cladophora vagabunda有很高的序列同源性,但是形态特征却差异很大。从显微结构结果来看,五个岩溶泉域采集到的刚毛藻在细胞直径上无显著差异,藻体的形态特征与脆弱刚毛藻相一致。但是,岩溶泉域采集的藻体细胞直径比文献报道中在湖泊和河流中采集的脆弱刚毛藻直径要大。另外,仅在两个地点(XA和ST)采集的标本中发现有假根状分枝。因此,基于形态学和分子序列的结果,将这五个泉域的刚毛藻鉴定为脆弱刚毛藻(Cladophora fracta)。     

Probiotic and other functional microbes: from markets to mechanisms

Insight into the diversity and function of the human intestinal microbiota has been stimulated by clinical studies with bacteria that exhibit specific functions and which are marketed as probiotics to positively affect our health. Initial efforts concentrated on establishing sound scientific support for the efficacy of these probiotic bacteria, which mainly include Lactobacillus and Bifidobacterium species. Following these evidence-based functional approaches, considerable research is now focused on the mechanisms of action of probiotic bacteria. The mechanisms identified to date mainly relate to the stimulation of host defence systems, immune modulation and the competitive exclusion of pathogens. Recent efficacy, molecular and genomics-based studies have also been reported for some probiotic strains that have found their position in the market place.     

未培养微生物分离培养技术研究进展

自然环境中的微生物具有多样性高的特点,而99%的微生物使用传统的方法仍然是"不可培养的",并且能被培养的小部分微生物不能够代表微生态的多样性。因此,确定新的微生物物种和功能仍然是目前的重要任务。本文将综述基于调整培养基、考虑微生物间相互作用、捕获分离培养、高通量分离培养来分离培养微生物群体中的未培养微生物的方法,及功能性研究的进展情况。     

Use of isotopic and molecular techniques to link toluene degradation in denitrifying aquifer microcosms to specific microbial populations

Microcosms were inoculated with sediments from both a petroleum-hydrocarbon (PHC)-contaminated aquifer and from a nearby pristine aquifer and incubated under anoxic denitrifying conditions with [methyl-13C]toluene. These microcosms served as a laboratory model system to evaluate the combination of isotope (13C-labeling of polar-lipid-derived fatty acids) and molecular techniques (16S rRNA-targeting gene probes) to identify the toluene-metabolizing population. After total depletion of toluene, the following bacterial phospholipid fatty acids (PLFA) were 13C-enriched: 16:1omega7c, 16:1omega7t, 16:0, cy17:0, and 18:1omega7c. Pure culture experiments demonstrated that these compounds were also found in PLFA profiles of PHC-degrading Azoarcus spp. (beta-Proteobacteria) and related species. The origin of the CO2 evolved in the microcosms was determined by measurements of stable carbon isotope ratios. Toluene represented 11% of the total pool of mineralized substrates in the contaminated sediment and 54% in the pristine sediment. The microbial community in the microcosm incubations was characterized by using DAPI staining and whole-cell hybridization with specific fluorescently labeled 16S rRNA-targeted oligonucleotide probes. Results revealed that 6% of the DAPI-stained cells in the contaminated sediment and 32% in the pristine sediment were PHC-degrading Azoarcus spp. In biotic control microcosms (incubated under denitrifying conditions, no toluene added), Azoarcus spp. cells remained at less than 1% of the DAPI-stained cells. The results show that isotope analysis in combination with whole-cell hybridization is a promising approach to identify and to quantify denitrifying toluene degraders within microbial communities.     

Using respirometric techniques and fluorescent in situ hybridization to evaluate the heterotrophic active biomass in activated sludge

The separation and accurate quantification of active biomass components in activated sludge is of paramount importance in models, used for the management and design of waste water (WW) treatment plants. Accurate estimates of microbial population concentrations and the direct, in situ determination of kinetic parameters could improve the calibration and validation of existing models of biological nutrient removal activated sludge systems. The aim of this study was to obtain correlations between heterotrophic active biomass (Z(BH)) concentrations predicted by mathematical models and quantitative information obtained by Fluorescent in situ hybridizations (FISH). Respirometric batch test were applied to mixed liquors drawn from a well-defined parent anoxic/aerobic activated sludge system to quantify the Z(BH) concentrations. Similarly fluorescent labeled, 16S rRNA-targeted oligonucleotide probes specific for ammonia and nitrite oxidizers were used in combination with DAPI staining to validate the Z(BH) active biomass component in activate sludge respirometric batch tests. For the direct enumeration and simultaneous in situ analysis of the distribution of nitrifying bacteria, in situ hybridization with oligonucleotide probes were used. Probes (NSO 1225, NSR 1156, and NIT3) were used to target the nitrifiers and the universal probe (EUB MIX) was used to target all Eubacteria. Deducting the lithoautotrophic population from the total bacteria population revealed the Z(BH) population. A conversion factor of 8.49 x 10(-11) mg VSS/cell was applied to express the Z(BH) in terms of COD concentration. Z(BH) values obtained by molecular probing correlated closely with values obtained from the modified batch test. However, the trend of consistently poor correspondence of measured and theoretical concentrations were evident. Therefore, the focus of this study was to investigate alternative technology, such as FISH to validate or replace kinetic parameters which are invariably incorporated into models.     

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2 concentrations

As in many deep underground environments, the microbial communities in subsurface high‐CO₂ ecosystems remain relatively unexplored. Recent investigations based on single‐gene assays revealed a remarkable variety of organisms from little studied phyla in Crystal Geyser (Utah, USA), a site where deeply sourced CO₂‐saturated fluids are erupted at the surface. To provide genomic resolution of the metabolisms of these organisms, we used a novel metagenomic approach to recover 227 high‐quality genomes from 150 microbial species affiliated with 46 different phylum‐level lineages. Bacteria from two novel phylum‐level lineages have the capacity for CO₂ fixation. Analyses of carbon fixation pathways in all studied organisms revealed that the Wood‐Ljungdahl pathway and the Calvin‐Benson‐Bassham Cycle occurred with the highest frequency, whereas the reverse TCA cycle was little used. We infer that this, and selection for form II RuBisCOs, are adaptions to high CO₂‐concentrations. However, many autotrophs can also grow mixotrophically, a strategy that confers metabolic versatility. The assignment of 156 hydrogenases to 90 different organisms suggests that H₂ is an important inter‐species energy currency even under gaseous CO₂‐saturation. Overall, metabolic analyses at the organism level provided insight into the biochemical cycles that support subsurface life under the extreme condition of CO₂ saturation.