Higher Bacterial Biomass Research Articles

Distribution, community structure and metabolic potential of bacterioplankton in a small boreal lake: Microscopy-based survey and 16S rRNA-based DNA metabarcoding

Bacteria are numerous and diverse organisms that have a significant impact on the functioning of aquatic ecosystems. On the vast territory of the West Siberian Lowland (Russia) there are many rivers, lakes and bogs, the microbial communities of which are almost unexplored. Here, we report the study results on the distribution, diversity, community structure and functions of bacterioplankton in the pelagic and littoral zones of one of the lakes, located in this region (Lake Kuchak) obtained using microscopic techniques and 16S rRNA gene metabarcoding. The high total bacterial abundance and biomass, the diversity indices, and the high number of Actinobacteria amplicon sequence variants (ASVs), along with the relatively low number of Betaproteobacteria ASVs, indicate the eutrophication of the lake, especially in its overgrown littoral zone. Similar bacterial communities developed in the pelagic and littoral zones due to similar environmental conditions in these habitats of this small and shallow lake. Nevertheless, there were some differences between the pelagic and littoral zones, causing differences in the bacterial communities of these zones more in size and morphological structure than in taxonomic composition. Comparative analysis of the bacterial metabolic ways showed the higher functional potential in the pelagic zone compared to the littoral one. Signs of methylotrophic and methanotrophic activities, as well as pollutant biodegradation potential of the bacterioplankton were identified. The bacterial distribution and community composition indicates the input of organic substances into the lake from the watershed, but also shows the community resistance to allochthonous microorganisms. Alpha diversity indices, distribution of taxonomic groups and some other results indicate deterioration of water quality in the overgrown littoral zone.

Comparison of water quality, planktonic community, and volatile organic compounds in the seawater from five cage culture areas of large yellow croaker

The rapid development of marine fish cage farming has led to ecological damage, adversely affecting fish quality. Significant regional quality differences in large yellow croaker under similar farming conditions suggest that the water environment plays a crucial role in fish quality. Using full-length18s/16 s rRNA sequencing with bacterial absolute quantity and headspace solid-phase microextraction coupled with gas chromatography mass spectrometry (HS-SPME-GC–MS), we investigated the planktonic community and volatile organic compounds (VOCs) in seawater from cages housing large yellow croaker at five major mariculture sites in China, including ND (26.627°E, 119.638°N), NJ (27.479°E, 121.052°N), DT (27.981°E, 121.196°N), NC (28.470°E, 121.907°N), and DJ (30.198°E, 122.698°N). Notably, three dominant ciliates, Mesodinium rubrum, Strombidium sp., and Pseudotontonia simplicidens, were identified in NJ as bioindicators for water quality. Additionally, NJ cages had the highest bacterial biomass with 54 % Synechococcus CC9902, and the lowest abundance of bacteria with pathogenic activities. These may explain NJ's optimal water quality parameters and the highest eukaryotic biodiversity. In contrast, DT and DC contained only the core ciliate M. rubrum, with no dominant ciliate in ND. Styela gibbsii, a filter feeder, predominated in ND cages, adhering to the net. The occurrence of red tide-causing species and pathogenic bacteria or fungi was notable in DJ, DC, DT, and ND, including Akashiwo sanguinea, an unclassified Dinophyceae, Gyrodinium fusiforme, Pirum gemmate, Candida parapsilosis, Hortaea werneckii, and Pseudomonas juntendi. Bacterial functional analysis showed that ND cages harbored unique strains linked to ureolysis and various pathogenic activities. Co-association networks suggested that 2,4-Di-tert-butylphenol and pentadecane might play roles in communication within plankton communities. A rise in pleasant VOCs such as acetyl valeryl, pentadecane, butyl butyrate, tetradecane, and 5-butyldihydro-2(3H)-furanone was observed in DJ, DC, DT, and NJ, compared to ND. The results provide valuable insights for improving aquaculture practices and mitigating environmental impacts. The results provide valuable bioindicators for monitoring water quality using microbial communities and VOC profiles.

The Impact of Candida albicans in the Development, Kinetics, Structure, and Cell Viability of Biofilms on Implant Surfaces-An In Vitro Study with a Validated Multispecies Biofilm Model.

This study aimed to evaluate the impact of Candida albicans on subgingival biofilm formation on dental implant surfaces. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to compare biofilm structure and microbial biomass in the presence and absence of the fungus after periods of 24, 48, and 72 h. Quantitative polymerase chain reaction (qPCR) was used to quantify the number of viable and total micro-organisms for each of the biofilm-forming strains. A general linear model was applied to compare CLSM and qPCR results between the control and test conditions. The biofilm developed with C. albicans at 72 h had a higher bacterial biomass and a significantly higher cell viability (p < 0.05). After both 48 and 72 h of incubation, in the presence of C. albicans, there was a significant increase in counts of Fusobacterium nucleatum and Porphyromonas gingivalis and in the cell viability of Streptococcus oralis, Aggregatibacter actinomycetemcomitans, F. nucleatum, and P. gingivalis. Using a dynamic in vitro multispecies biofilm model, C. albicans exacerbated the development of the biofilm grown on dental implant surfaces, significantly increasing the number and cell viability of periodontal bacteria.

Dissolved carbohydrates and its influence on bacterioplankton diversity in the euphotic zone of Equatorial Indian Ocean during southwest monsoon

The Equatorial Indian Ocean (EIO) is oligotrophic in nature, low in productivity and characterised by relatively high bacterial biomass and heterotrophic productivity. The microbial biomass is fuelled by dissolved organic carbon (DOC) whose lability depends upon its chemistry. During an expedition in the EIO, samples for dissolved carbohydrates (DCHO), dissolved monosaccharide (MCHO), dissolved polysaccharide (PCHO), total bacterial abundance, total organic carbon (TOC), nutrients, chlorophyll a (chl a), bacterial diversity, and phytoplankton composition were estimated along two transects (TS-1 & TS-2) in the euphotic depth (200 m). DCHO and MCHO samples were analysed using 3-methyl-2-benzothiozolinone hydrazone hydrochloride (MBTH) method. The DCHO, MCHO, and PCHO concentrations in TS-1 ranged from 2.4 to 5.8 μM; 0.7 to 2.7 μM; 0.7 to 3.4 μM, while in TS-2 it ranged from 2.2 to 4.8 μM; 0.3 to 2.8 μM; 0.2 to 3.8 μM, respectively. Vertically, DCHO concentrations decreased within the photic depths in most stations. PCHO concentrations were relatively greater in TS-2 than TS-1, which may be due to preferential removal of MCHO in TS-2. In the top 200 m of the water column, Proteobacteria was the most abundant bacterial phylum followed by Cyanobacteria, Actinobacteriota, Bacteroidota, and SAR-324 while dinoflagellates dominated the phytoplankton population. The distribution of DCHO and PCHO were inversely correlated to salinity, temperature, and chl a. The bacterial heterotrophs like alpha-Proteobacteria, Chloroflexii, and Verrumicrobiota along with SAR324 and Actinobacteriota were clustered with nutrients, while Bdellovibriota and Dadabacteria clustered with MCHO, PCHO, and DCHO. These results highlight the impact of DCHO & PCHO lability on the distribution of bacterial community and delineate oceanographic factors that regulate the distribution of DCHO and its constituents in EIO waters.

Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study

Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.

Current ocular microbiome investigations limit reproducibility and reliability: Critical review and opportunities

Enthusiasm for research describing microbial communities using next-generation sequencing (NGS) has outpaced efforts to standardize methodology. Without consistency in the way research is carried out in this field, the comparison of data between studies is near impossible and the utility of results remains limited. This holds true for bacterial microbiome research of the ocular surface, and other sites, in both humans and animals. In addition, the ocular surface remains under-explored when compared to other mucosal sites. Low bacterial biomass samples from the ocular surface lead to further technical challenges. Taken together, two major problems were identified: (1) Normalization of the workflow in studies utilizing NGS to investigate the ocular surface bacteriome is necessary in order to propel the field forward and improve research impact through cross-study comparisons. (2) Current microbiome profiling technology was developed for high bacterial biomass samples (such as feces or soil), posing a challenge for analyses of samples with low bacterial load such as the ocular surface. This article reviews the challenges and limitations currently facing ocular microbiome research and provides recommendations for minimum reporting standards for veterinary ophthalmologists and clinician scientists to limit inter-study variation, improve reproducibility, and ultimately render results from these studies more impactful. The move toward normalization of methodology will expedite and maximize the potential for microbiome research to translate into meaningful discovery and tangible clinical applications.

Differences in airway microbiome and metabolome of single lung transplant recipients

BackgroundRecent studies suggest that alterations in lung microbiome are associated with occurrence of chronic lung diseases and transplant rejection. To investigate the host-microbiome interactions, we characterized the airway microbiome and metabolome of the allograft (transplanted lung) and native lung of single lung transplant recipients.MethodsBAL was collected from the allograft and native lungs of SLTs and healthy controls. 16S rRNA microbiome analysis was performed on BAL bacterial pellets and supernatant used for metabolome, cytokines and acetylated proline-glycine-proline (Ac-PGP) measurement by liquid chromatography-high-resolution mass spectrometry.ResultsIn our cohort, the allograft airway microbiome was distinct with a significantly higher bacterial burden and relative abundance of genera Acinetobacter & Pseudomonas. Likewise, the expression of the pro-inflammatory cytokine VEGF and the neutrophil chemoattractant matrikine Ac-PGP in the allograft was significantly higher. Airway metabolome distinguished the native lung from the allografts and an increased concentration of sphingosine-like metabolites that negatively correlated with abundance of bacteria from phyla Proteobacteria.ConclusionsAllograft lungs have a distinct microbiome signature, a higher bacterial biomass and an increased Ac-PGP compared to the native lungs in SLTs compared to the native lungs in SLTs. Airway metabolome distinguishes the allografts from native lungs and is associated with distinct microbial communities, suggesting a functional relationship between the local microbiome and metabolome.

Assessing the Microbial Communities in Four Different Daqus by Using PCR-DGGE, PLFA, and Biolog Analyses.

Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

Treatment of Port Harcourt Refinery Effluent by a Bacterial Consortium Immobilized on Agro-based Bio Carriers

Discharge of poorly treated refinery wastewater has always been a major environmental challenge. Bacterial immobilization is key to the maintenance of biomass on a contaminated site. In this study, a mixed culture of three bacterial isolates from oil-polluted water: Pseudomonas aeruginosa (MN294989), Bacillus tequilensis (MN294990) and Micrococcus sp. immobilized on Groundnut Shell (GS), Melon Husk (MH) and Sugarcane Bagasse (SB) were employed in the bioremediation of Port Harcourt refinery wastewater. Surface area and pore size distribution of the agro-based bio carriers were suitable for bacteria adhesion. The bacterial isolates were screened for phenol, naphthalene and hydrocarbon utilization. Scanning Electron Microscopy (SEM) was used to ascertain the immobilization of the consortium on the agro-base carriers. A 15-days laboratory-scale treatment of refinery raw wastewater was compared in the immobilised and immobilized consortium. The agro-based residue immobilized consortium enhanced the reduction in BOD5, COD, oil and grease, phenol by 7%, 9%, 30% and 5% respectively compared to the free form of the consortium. This study underscores the role of immobilization in maintaining high bacterial biomass on contaminated site and possible improvement in bioremediation of refinery wastewater.

Microbial generation of elemental mercury from dissolved methylmercury in seawater.

Elemental mercury (Hg0) formation from other mercury species in seawater results from photoreduction and microbial activity, leading to possible evasion from seawater to overlying air. Microbial conversion of monomethylmercury (MeHg) to Hg0 in seawater remains unquantified. A rapid radioassay method was developed using gamma-emitting 203Hg as a tracer to evaluate Hg0 production from Hg(II) and MeHg in the low pM range. Bacterioplankton assemblages in Atlantic surface seawater and Long Island Sound water were found to rapidly produce Hg0, with production rate constants being directly related to bacterial biomass and independent of dissolved Hg(II) and MeHg concentrations. About 32% of Hg(II) and 19% of MeHg were converted to Hg0 in 4 d in Atlantic surface seawater containing low bacterial biomass, and in Long Island Sound water with higher bacterial biomass, 54% of Hg(II) and 8% of MeHg were transformed to Hg0. Decreasing temperatures from 24°C to 4°C reduced Hg0 production rates cell-1 from Hg(II) 3.3 times as much as from a MeHg source. Because Hg0 production rates were linearly related to microbial biomass and temperature, and microbial mercuric reductase was detected in our field samples, we inferred that microbial metabolic activities and enzymatic reactions primarily govern Hg0 formation in subsurface waters where light penetration is diminished.

Distribution and ecology of living (Rose Bengal stained) Marsipella elongata Norman 1878 (Foraminifera) in the Campos Basin, southeastern Brazilian continental margin

The distribution of the agglutinated benthic foraminifer Marsipella elongata is studied from 70 oceanographic stations, located between 400m and 3000m depth in the Campos Basin (southeastern Brazilian continental margin). Samples of the upper 0–2 cm of surficial sediment were collected during two sampling campaigns in 2008 and 2009. Grain size, total organic carbon, total nitrogen, calcium carbonate, phytopigment, lipids biomarkers (sterols, fatty acids and n-alcohols), total lipids, and bacterial biomass are analyzed as environmental parameters. These data as well as the particulate organic matter flux to the sea floor are compared with the distribution of living (rose Bengal stained) Marsipella elongata. Living specimens of M. elongata occur in the range of 400–3000mwater depth. The distribution of this species appears to be related to relatively high particulate organic matter vertical flux, phytopigment content, and bacterial biomass under the influence of Brazil Current, Intermediate Western Boundary Current and Deep Western Boundary Current conditions (0.3–0.8 m/s).

Microbial plankton communities in the coastal southeastern Black Sea: biomass, composition and trophic interactions

Summary We investigated biomass and composition of the pico-, nano- and microplankton communities in a coastal station of the southeastern Black Sea during 2011. We also examined trophic interactions within these communities from size-fractionated dilution experiments in February, June and December. Autotrophic and heterotrophic biomasses showed similar seasonal trends, with a peak in June, but heterotrophs dominated throughout the year. Autotrophic biomass was mainly comprised by nanoflagellates and diatoms in the first half of the year, and by dinoflagellates and Synechococcus spp. in the second half. Heterotrophic biomass was mostly dominated by heterotrophic bacteria, followed by nanoflagellates and microzooplankton. Dilution experiments suggest that nano- and microzooplankton were significant consumers of autotrophs and heterotrophic bacteria. More than 100% of bacterial production was consumed by grazers in all experiments, while 46%, 21% and 30% of daily primary production were consumed in February, June and December, respectively. In February, autotrophs were the main carbon source, but in December, it was heterotrophic bacteria. An intermediate situation was observed in June, with similar carbon flows from autotrophs and heterotrophic bacteria. Size-fraction dilution experiments suggested that heterotrophic nanoflagellates are an important link between the high heterotrophic bacterial biomass and microzooplankton. In summary, these results indicate that nano- and microzooplankton were responsible for comprising a significant fraction of total microbial plankton biomass, standing stocks, growth and grazing processes. This suggests that in 2011, the microbial food web was an important compartment of the planktonic food web in the coastal southeastern Black Sea.

Effect of bacteria on growth and biochemical composition of two benthic diatoms Halamphora coffeaeformis and Entomoneis paludosa

Benthic diatoms are the dominant microalgae in intertidal mudflats and are in constant interaction with their surrounding bacteria. This study was designed to investigate the effect of bacteria on growth, biomass, elemental (C & N) and biochemical composition, and extracellular polymeric substances (EPS) excretion by two marine benthic diatoms, Halamphora coffeaeformis and Entomoneis paludosa. The experiments were conducted on diatom cultures previously exposed or not to antibiotics. The treatment with antibiotics caused a decrease of bacterial abundance from 24 to fewer than 1 bacteria per algal cell. In non-treated cultures of E. paludosa and H. coffeaeformis, the bacteria phylogenetic affiliation was equally distributed between Bacteroidetes (Flavobacteriia) and Proteobacteria (alpha- and gammaproteobacteria). After treatment with antibiotics, the residual bacterial community was ~37% Flavobacteriia (Winogragskyella genus), 34% for the alphaproteobacteria (mainly Roseibacterium sp and Antarctobacter sp.) and 29% for the gammaproteobacteria (mainly Methylophaga sp. and Stenotrophomonas sp.). Growth of H. coffeaeformis and E. paludosa in non-treated cultures was enhanced by the abundance of the associated bacteria, with mean growth rate of 1day−1 compared to 0.7 for antibiotic treated cultures. In E. paludosa, maximal cell abundance was higher in the presence of bacteria while the final carbon biomass did not vary, but in H. coffeaeformis maximal cell abundance did not vary significantly while final carbon biomass was higher in the presence of bacteria. By contrast, for both diatoms, cellular content of protein and lipids decrease significantly, as did extracellular carbon (EPS fraction) in the presence of bacteria. However, only a minor effect was observed on cellular carbohydrates, C/N ratio, and pigments (Chl a). Diatoms carbon fluxes towards the main biochemical components were also modified, with the protein carbon fraction significantly lower relative to other carbon compounds in the presence of high bacterial biomass. These results showed the complex interactions between diatoms and their associated bacteria. Promotion of diatoms growth by the presence of bacteria appears linked to change in microalgae biochemical composition that will modify the biofilm. Our results might help understanding the regulation of benthic biota in mudflat ecosystems.

Luffa sponge offsets the negative effects of aeration on bacterial cellulose production.

To offset the negative effects of aeration on bacterial cellulose (BC) production by acetic acid bacteria using enmeshed cellulose microfibrils (CM) on luffa sponge matrices (LSM). The CM were enmeshed on LSM (LSM-CM). The optimal amount of LSM-CM was determined for BC production under aerated conditions. Without LSM-CM, no BC was produced in seven out of nine production cycles at the highest aeration rate (9lmin-1 ). However, with 0·5% LSM-CM and an aeration rate of 3lmin-1 , a satisfactory oxygen transfer coefficient was achieved, and also a good yield of BC (5·24gl-1 ). Moreover, the LSM-CM was able to be recycled through nine consecutive BC production cycles. The highest BC yields (from 5·8±0·4 to 6·6±0·4gl-1 ) were associated with high bacterial biomass and this was confirmed by scanning electron microscopy. We confirm that LSM-CM works well as a starter. Microenvironments low in dissolved oxygen within the matrices of LSM-CM are important for BC production under aeration conditions. The LSM-CM provides a microenvironment which offsets the negative effects of aeration on BC production. A sustainable, economic process for mass BC production is described using recycled LSM-CM with aeration.

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community.

Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short-term studies, and the guild of mycelium decomposers has been poorly defined. Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21wk. The community of associated microbes and enzymatic processes in this specific substrate were described. The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer-degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r-strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others. Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community.

Modelling bioclogging in variably saturated porous media and the interactions between surface/subsurface flows: Application to Constructed Wetlands

Horizontal subsurface Flow Constructed Wetlands (HF CWs) are biofilters planted with aquatic macrophytes within which wastewater is treated mostly through contact with bacterial biofilms. The high concentrations of organic carbon and nutrients being transported leads to high bacterial biomass production, which decreases the flow capacity of the porous material (bioclogging). In severe bioclogging scenarios, overland flow may take place, reducing overall treatment performance. In this work we developed a mathematical model using COMSOL Multiphysics™ and MATLAB® to simulate bioclogging effects in HF CWs. Variably saturated subsurface flow and overland flow were described using the Richards equation. To simplify the inherent complexity of the processes involved in bioclogging development, only one bacterial group was considered, and its growth was described using a Monod equation. Bioclogging effects on the hydrodynamics were taken into account by using a conceptual model that affects the value of Mualem's unsaturated relative permeability. Simulation results with and without bioclogging were compared to showcase the impact of this process on the overall functioning of CWs. The two scenarios rendered visually different bacteria distributions, flow and transport patterns, showing the necessity of including bioclogging effects on CWs models. This work represents one of the few studies available on bioclogging in variably saturated conditions, and the presented model allows simulating the interaction between overland and subsurface flow occurring in most HF CWs. Hence, this work gets us a step closer to being able to describe CWs functioning in an integrated way using mathematical models.

Use of dispersant in mudflat oil-contaminated sediment: behavior and effects of dispersed oil on micro- and macrobenthos.

The present study aimed to examine whether the use of dispersant would be suitable for favoring the hydrocarbon degradation in coastal marine sediments without impacting negatively micro- and macrobenthic organisms. Mudflat sediments, maintained during 286 days in mesocosms designed to simulate natural conditions, were contaminated or not with Ural blend crude oil (REBCO) and treated or not with third-generation dispersant (Finasol OSR52). While the dispersant did not lead to an increase of hydrocarbon biodegradation, its use enables an attenuation of more than 55 % of the sediment concentration of total petroleum hydrocarbons (TPH). Canonical correspondence analysis (CCA) correlating T-RFLP patterns with the hydrocarbon content and bacterial abundance indicated weak differences between the different treatments except for the mesocosm treated with oil and dispersant for which a higher bacterial biomass was observed. The use of the dispersant did not significantly decrease the macrobenthic species richness or macroorganisms' densities in uncontaminated or contaminated conditions. However, even if the structure of the macrobenthic communities was not affected, when used in combination with oil, biological sediment reworking coefficient was negatively impacted. Although the use of the dispersant may be worth considering in order to accelerate the attenuation of hydrocarbon-contaminated mudflat sediments, long-term effects on functional aspects of the benthic system such as bioturbation and bacterial activity should be carefully studied before.

Probiotics: from the lab to the consumer

In the last years, the field of probiotics has grown notably. However, out of the thousands of strains isolated each year in the labs around the world, very few enter in a phase of industrial development and even a lower number go to the market. In this article, the main aspects that have to be taken into account in the, usually, long and winding road that a strain must follow from isolation to the market are reviewed Results and conclusions: A probiotic microorganism has to be correctly identified at the species and strain levels. The genome sequence is the gold identification standard and provides valuable information on the safety, functionality and technological properties of a strain. The cases in which a link between a probiotic and an adverse effect has been established are scarce and have involved people with underlying pathologies. There is a wide variety of in vitro, ex vivo and animal model assays for the screening of probiotics, which provide useful information throughout the selection process; however, correctly designed clinical trials are the only way to obtain direct results on the safety and efficacy of a probiotic to the target population. Probiotic companies have the need to obtain a very high bacterial biomass in an economically viable manner while preserving the concentration of live bacteria required for exerting the expected beneficial effect until the end of the probiotic's shelf life. Finally, commercial aspects play a key role in the decision of starting an industrial development and, eventually, to place a probiotic in the market.

Massive regime shifts and high activity of heterotrophic bacteria in an ice-covered lake.

In winter 2009/10, a sudden under-ice bloom of heterotrophic bacteria occurred in the seasonally ice-covered, temperate, deep, oligotrophic Lake Stechlin (Germany). Extraordinarily high bacterial abundance and biomass were fueled by the breakdown of a massive bloom of Aphanizomenon flos-aquae after ice formation. A reduction in light resulting from snow coverage exerted a pronounced physiological stress on the cyanobacteria. Consequently, these were rapidly colonized, leading to a sudden proliferation of attached and subsequently of free-living heterotrophic bacteria. Total bacterial protein production reached 201 µg C L−1 d−1, ca. five times higher than spring-peak values that year. Fluorescence in situ hybridization and denaturing gradient gel electrophoresis at high temporal resolution showed pronounced changes in bacterial community structure coinciding with changes in the physiology of the cyanobacteria. Pyrosequencing of 16S rRNA genes revealed that during breakdown of the cyanobacterial population, the diversity of attached and free-living bacterial communities were reduced to a few dominant families. Some of these were not detectable during the early stages of the cyanobacterial bloom indicating that only specific, well adapted bacterial communities can colonize senescent cyanobacteria. Our study suggests that in winter, unlike commonly postulated, carbon rather than temperature is the limiting factor for bacterial growth. Frequent phytoplankton blooms in ice-covered systems highlight the need for year-round studies of aquatic ecosystems including the winter season to correctly understand element and energy cycling through aquatic food webs, particularly the microbial loop. On a global scale, such knowledge is required to determine climate change induced alterations in carbon budgets in polar and temperate aquatic systems.

Growth-promoting effects of pepsin- and trypsin-treated caseinomacropeptide from bovine milk on probiotics.

Probiotic Lactobacillus and Bifidobacterium species are generally fastidious bacteria and require rich media for propagation. In milk-based media, they grow poorly, and nitrogen supplementation is required to produce high bacterial biomass levels. It has been reported that caseinomacropeptide (CMP), a 7-kDa peptide released from κ-casein during renneting or gastric digestion, exhibits some growth-promoting activity for lactobacilli and bifidobacteria. During the digestive process, peptides derived from CMP are detected in the intestinal lumen The aim of this study was to evaluate the effects of peptic and tryptic digests of CMP on probiotic lactic acid bacteria growth in de Man, Rogosa and Sharpe broth (MRS) and in milk during fermentation at 37 °C under anaerobic conditions. The study showed that pepsin-treated CMP used as supplements at 0.5 g/l can promote the growth of probiotics even in peptone-rich environments such as MRS. The effect was strain-dependent and evident for the strains that grow poorly in MRS, with an improvement of >1.5 times (P<0.05) by addition of pepsin-treated CMP. Trypsin-treated CMP was much less efficient as growth promoter. Moreover, pepsin-treated CMP was effective in promoting the growth in milk of all probiotic lactic acid bacteria tested, with biomass levels being improved significantly, by 1.7 to 2.6 times (P<0.05), depending on the strain. Thus, supplementation of MRS and of milk with pepsin-treated CMP would be advantageous for the production of high biomass levels for Bifidobacteria and Lactobacilli.