Individual-based modelling of invasion in bioaugmented sand filter communities

Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synthesizing these effects into a competition structure for our model. Pairwise competition outcomes are determined based on interaction effects in terms of functionality. We also consider non-deterministic competition, where winning probabilities are assigned based on the relative intrinsic competitiveness of each strain. Our model is able to reproduce the key qualitative dynamics observed in in vitro experiments with similar synthetic sand filter communities. Simulation outcomes can be explained based on the underlying competition structures and the resulting spatial dynamics. Our results highlight the importance of community diversity and in particular evenness in stabilizing the community dynamics, allowing us to study the establishment and development of these communities, and thereby illustrate the potential of the individual-based modelling approach for addressing microbial ecological theories related to synthetic communities

Aminobacter sp MSH1 invades sand filter community biofilms while retaining 2,6-dichlorobenzamide degradation functionality under C- and N-limiting conditions

Aminobacter sp. MSH1 is of interest for bioaugmentation of biofiltration units in drinking water treatment plants (DWTPs) due to its ability to degrade the groundwater micropollutant 2,6-dichlorobenzamide (BAM). Using a continuous flow chamber biofilm model, MSH1 was previously shown to colonize surfaces and degrade BAM at trace concentrations as low as 1 mu g/L under the oligotrophic conditions found in DWTPs. In DWTP filtration units, MSH1 has to compete with the resident biofilm microbiota for space and nutrients. Using the same model, we examined how a sand filter community (SFC) affects MSH1's BAM-degrading activity and biofilm formation under C-and N-limiting conditions when fed with trace concentrations of BAM. MSH1 was inoculated simultaneously with the SFC (co-colonization mode) or after the SFC formed a biofilm (invasion mode). MSH1 successfully established in the SFC biofilm showing growth and activity. In co-colonization mode, MSH1 decreased in number in the presence of the SFC and formed isolated colonies, while specific BAM-degradation activity increased. In the invasion mode, MSH1 also decreased in numbers in the presence of the SFC but formed mixed colonies, while specific BAM degradation was unaffected. Our results show that MSH1 invades and performs successfully in an SFC biofilm under the oligotrophic conditions of DWTPs

Трендсеттінг як ключовий фактор управління інноваційними ризиками індустрії моди

Індустрія моди нового тисячоріччя перетворилася в багатомільйонний сектор економіки, у котрому інноваційна діяльність грає ключову роль. Інновації в дизайні сучасного костюма з інструмента вдосконалювання характеристик об’єкта перетворюються в одну з основних його характеристик, тому фешн-проекти є інноваційними за своєю природою [2]

Dynamics of an Oligotrophic Bacterial Aquifer Community during Contact with a Groundwater Plume Contaminated with Benzene, Toluene, Ethylbenzene, and Xylenes: an In Situ Mesocosm Study{dagger}

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contaminatio

PHÂN TÍCH DI TRUYỀN KHẢ NĂNG DI CHUYỂN THEO PHENANTHRENE CỦA VI KHUẨN PSEUDOMONAS STUTZERI E1

ABSTRACTPseudomonas stutzeri strain E1 shows a two-time accelerated swarming behavior in minimal medium with sprayed phenanthrene in swimming assays and a five-time higher chemotaxis towards dissolved phenanthrene in capillary assays.  A mutant bank of strain E1 was constructed using the pTnMod-OGm plasposon mutagenesis system.  82 out of 2639 electroporants screened showed an altered phenotype of phenanthrene-driven motility and/or phenanthrene degradation. 16 representative mutants were selected for sequencing the genes flanking the plasposon insertion. Mutations in flhA resulted in abolished swimming and swarming phenotype, and in flgK resulted in abolished swimming and diminished swarming phenotype.  A mutation in cheY performed abolished swimming and reduced swarming activity while a gidA mutation resulted in decreased phenanthrene degradation and both decreased swimming and swarming behavior. A mutation in gene encoding a Zn dependent protease and in a gene encoding capsular polysaccharide biosynthesis protein resulted in abolished swarming suggesting that these proteins also play a potential role in the swarming activity of P. stutzeri E1.Keywords: Pseudomonas stutzeri, polycyclic aromatic hydrocarbon, phenanthrene, chemotaxis, plasposon pTnMod-OGm, swimming, swarmingTitle: Genetic analysis of phenanthrene-driven motility by the phenanthrene-degrading soil isolate Pseudomonas stutzeri E1TóM TắTPseudomonas stutzeri dòng E1 có khả năng di chuyển bề mặt tăng gấp đôi khi nuôi trong môi trường tối thiểu được phủ phenanthrene.  Thí nghiệm mao dẫn cũng cho thấy E1 di chuyển nhanh gấp năm lần về hướng có phenanthrene.  Plasposon pTnMod-OGm được dùng để tạo thư viện đột biến dòng E1.  Trong số 2639 đột biến đã khảo sát, 82 đột biến biểu hiện những thay đổi về khả năng di chuyển theo phenanthrene và/hoặc phân hủy phenanthrene.  16 đột biến được chọn để giải trình tự của các gen đột biến tương ứng. Đột biến gen flhA làm E1 mất khả năng bơi và di chuyển bề mặt, đột biến gen flgK làm mất khả năng bơi và giảm khả năng di chuyển bề mặt của E1.  Đột biến gen cheY làm mất khả năng bơi và giảm khả năng di chuyển bề mặt trong khi đột biến gen gidA làm giảm khả năng phân hủy phenanthrene và giảm cả khả năng bơi và di chuyển bề mặt của E1.  Đột biến gen tổng hợp protein Zn-dependent protease và gen tổng hợp vỏ polysaccharide làm cho E1 mất khả năng di chuyển bề mặt chứng tỏ các protein này cũng giữ vai trò tiềm năng trong hoạt động di chuyển bề mặt của P. stutzeri E1.Từ khoá: Pseudomonas stutzeri, hydrocarbon đa vòng thơm, phenanthrene, hóa hướng động, plasposon pTnMod-OGm, bơi, di chuyển bề mặt</p

Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats

IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats

IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1-3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.Peer reviewe

Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats

IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are "hot spots" of plasmids potentially carrying catabolic genes.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecula