Medical biofilms

For more than two decades, Biotechnology and Bioengineering has documented research focused on natural and engineered microbial biofilms within aquatic and subterranean ecosystems, wastewater and waste-gas treatment systems, marine vessels and structures, and industrial bioprocesses. Compared to suspended culture systems, intentionally engineered biofilms are heterogeneous reaction systems that can increase reactor productivity, system stability, and provide inherent cell:product separation. Unwanted biofilms can create enormous increases in fluid frictional resistances, unacceptable reductions in heat transfer efficiency, product contamination, enhanced material deterioration, and accelerated corrosion. Missing from B&B has been an equivalent research dialogue regarding the basic molecular microbiology, immunology, and biotechnological aspects of medical biofilms. Presented here are the current problems related to medical biofilms; current concepts of biofilm formation, persistence, and interactions with the host immune system; and emerging technologies for controlling medical biofilms.     

河岸无脊椎动物多样性维持机制研究进展

河岸是河流与陆地之间重要的生态界面,生物多样性丰富,但受到人为活动的严重威胁。无脊椎动物在河岸生物多样性中占有重要地位,发挥着非常重要的生态功能,也是水生生态系统和陆地生态系统之间物质和能量联系的重要纽带。尽管已有很多学者对河岸无脊椎动物群落进行了研究,但缺乏对河岸无脊椎动物多样性维持机制的总结。本文结合洪水和干旱、营养物质、微生境多样性、河岸植被、微气候梯度、食物资源以及河流空间梯度等影响因素,初步讨论和归纳了河岸无脊椎动物多样性的维持机制。周期性洪水和干旱引发了无脊椎动物的繁殖和迁移等行为,增加了河岸无脊椎动物群落周转率,为无脊椎动物创造了理想的条件。充足的营养物质使河岸具有较高的初级生产力,支撑了较高的无脊椎动物多样性。较高的微生境多样性为无脊椎动物提供了多样的生态位空间,孕育了特殊的河岸无脊椎动物种类。复杂的河岸植物群落不但是河岸无脊椎动物的食物来源之一,也为河岸无脊椎动物提供了多样的生态位空间和重要的避难场所。微气候环境的空间分异提供了复杂多样的生境条件,为水生无脊椎动物和陆生无脊椎动物种类在河岸共存创造了条件。跨越界面的资源补给增加了河岸无脊椎动物的食物可利用率,为河岸无脊椎动物提供了特殊的食物来源。这些因素在空间上呈现出明显的纵向梯度和侧向梯度,从更大尺度上为河岸无脊椎动物的多样化提供了条件。因此,探讨河岸无脊椎动物多样性的维持机制对于河岸生物多样性保护以及河流生态系统综合管理具有重要的指导意义。     

全英文“环境工程微生物学”的国家线下一流本科课程成长之路

国家一流本科课程的评审认定是教育部全面深化教育教学改革的重要举措,也是提升本科教学质量的重要一环,极大地促进了任课教师对标评价量规进行教研教改。为促进环境工程专业核心基础课的教改,“环境工程微生物学”全英课程组在先进的教育思想、方法和教育心理学的指导下,对教学理念、课程内容、教学组织和实施等多方面进行了大胆的改革和创新,注重课程思政和因材施教,增加课堂教学的师生互动和生生互动;针对工科类学生的培养目标,引入实际工程的应用案例,在课内外补充环境微生物工程领域研究的最新进展和教师的科研成果,注重提升课程的高阶性、创新性和挑战度,从多方面强化知识、能力、素质的有机融合,学生学习效果明显提高。申报并获认定为首批国家线下一流本科课程和广东省一流本科课程。     

Influence of land consolidation on aquatic invertebrate communities and their distribution patterns in Korean rice fields

Rice fields, the major cropland in South Korea, provide an important wetland habitat for a diverse wildlife and contribute to biodiversity conservation. On the other hand, land consolidation conducted to increase agricultural production since the 1960s on a nationwide scale in South Korea has frequently been suggested to be one of the factors in the decline of biodiversity in agricultural ecosystems. Negative effects of habitat manipulation such as land consolidation would have influenced paddy field biodiversity, but the degree has not been clearly measured in South Korea. This study evaluated the impacts of land consolidation on the aquatic invertebrate biodiversity and investigated their patterns across the nation. Field sampling for biodiversity and environmental variables were made from 290 sites of paddy field over the country. Aquatic invertebrate communities were clustered into four major clusters showing land consolidation as the main factor and geographic location as the second factor. Species richness and abundance were significantly lower in the land consolidation fields (mean ± s.e., 12.80 ± 0.28 vs 88.89 ± 0.89 and 2027.15 ± 150.84 vs 2573.54 ± 572.16). Shannon diversity index was also significantly lower in land consolidation fields. Our results suggest that land consolidation and spatial location are important for biodiversity and conservation of the aquatic invertebrate assemblages in Korean rice fields.     

Electroactive biofilms: how microbial electron transfer enables bioelectrochemical applications

Microbial biofilms are ubiquitous. In marine and freshwater ecosystems, microbe–mineral interactions sustain biogeochemical cycles, while biofilms found on plants and animals can range from pathogens to commensals. Moreover, biofouling and biocorrosion represent significant challenges to industry. Bioprocessing is an opportunity to take advantage of biofilms and harness their utility as a chassis for biocommodity production. Electrochemical bioreactors have numerous potential applications, including wastewater treatment and commodity production. The literature examining these applications has demonstrated that the cell–surface interface is vital to facilitating these processes. Therefore, it is necessary to understand the state of knowledge regarding biofilms’ role in bioprocessing. This mini-review discusses bacterial biofilm formation, cell–surface redox interactions, and the role of microbial electron transfer in bioprocesses. It also highlights some current goals and challenges with respect to microbe-mediated bioprocessing and future perspectives.     

Developing a flexible learning activity on biodiversity and spatial scale concepts using open‐access vegetation datasets from the National Ecological Observatory Network

Biodiversity is a complex, yet essential, concept for undergraduate students in ecology and other natural sciences to grasp. As beginner scientists, students must learn to recognize, describe, and interpret patterns of biodiversity across various spatial scales and understand their relationships with ecological processes and human influences. It is also increasingly important for undergraduate programs in ecology and related disciplines to provide students with experiences working with large ecological datasets to develop students’ data science skills and their ability to consider how ecological processes that operate at broader spatial scales (macroscale) affect local ecosystems. To support the goals of improving student understanding of macroscale ecology and biodiversity at multiple spatial scales, we formed an interdisciplinary team that included grant personnel, scientists, and faculty from ecology and spatial sciences to design a flexible learning activity to teach macroscale biodiversity concepts using large datasets from the National Ecological Observatory Network (NEON). We piloted this learning activity in six courses enrolling a total of 109 students, ranging from midlevel ecology and GIS/remote sensing courses, to upper‐level conservation biology. Using our classroom experiences and a pre/postassessment framework, we evaluated whether our learning activity resulted in increased student understanding of macroscale ecology and biodiversity concepts and increased familiarity with analysis techniques, software programs, and large spatio‐ecological datasets. Overall, results suggest that our learning activity improved student understanding of biological diversity, biodiversity metrics, and patterns of biodiversity across several spatial scales. Participating faculty reflected on what went well and what would benefit from changes, and we offer suggestions for implementation of the learning activity based on this feedback. This learning activity introduced students to macroscale ecology and built student skills in working with big data (i.e., large datasets) and performing basic quantitative analyses, skills that are essential for the next generation of ecologists.     

A simple method to evaluate biofilm formation in exopolysaccharide-producing strains of Sinorhizobium meliloti

ABSTRACT

Sinorhizobium meliloti

is a bacterium of great agroeconomic importance because of its ability to fix atmospheric nitrogen in symbiotic association with alfalfa (Medicago sativa) roots, and it is often used in model studies. We investigated the effects of exopolysaccharides (EPSs) in cell-to-cell and cell-to-surface interactions in S. meliloti. The microtiter plate assay, a quantitative spectrophotometric method, is used to study bio?lm formation by bacterial adherence to an abiotic surface. It consists in staining biofilms grown in microtiter plates. Here, we describe two microbiology laboratory classes designed for undergraduate students of Experimental Biological Chemistry, in which they learn about biofilm forming capacity by observing the behavior of both wild-type and mutant strains of S. meliloti.     

It is about time: genetic variation in the timing of leaf‐litter inputs influences aquatic ecosystems

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Bacterial biofilms in a 'genes-to-ecosystems' context

In ecology, there is an increasing amount of research dedicated to understanding how intraspecific genetic diversity can extend beyond the population level to influence the assembly of communities and the functioning of ecosystems. In this issue of Molecular Ecology, Koh et al. (2012) take this exploration to a new level using bacterial biofilms and protozoan grazers. They show that there is heritable variation in the phenotypes of different variants of biofilms of Serratia marcescens and that these strains display complementarity when combined in a diverse assemblage. Mixtures of variants were significantly more resistant to protozoan grazing than either wild‐type or variant biofilms grown in monocultures. While similar biodiversity effects of genotype mixtures have been observed in other systems, Koh et al. (2012) link phenotype variation of the biofilms to a single nucleotide polymorphism in one regulatory gene. Importantly, the authors demonstrate that minimal changes in a genotype can result in substantial shifts in interspecific ecological interactions.     

微生物学全英文教学的意义、问题以及促研促教的实践探索北大核心CSCD

微生物涉及人类生活的方方面面,微生物学是各类高校为生命科学、医学、药学、农业、林业、食品等有关专业开设的本科生必修专业基础课。在国际化和一流学科发展趋势下,全英文授课具有重要意义并越来越受到重视。本文旨在探讨在如今面向人类生命健康、强调学科交叉的时代,如何结合本学校专业优势,开展微生物学英文教学的课程改革,将微生物学与医药、农业、环境、健康等充分结合,力争做到以学促研、以学促教,打造出具有本学校特色的微生物学全英文课程,将有关实践探索与微生物学教学工作者进行交流。     

Complex hydromorphology of meanders can support benthic invertebrate diversity in rivers

In freshwater environments, high biodiversity is commonly associated with habitat heterogeneity. River bends and meanders are particularly complex morphodynamic elements of watercourses. However, the specific spatio-temporal interactions between hydromorphology and the resident biota have scarcely been studied. This article reviews the relationships between hydraulic processes, and morphological units that are typical for meanders, and analyzes the concomitant spatial and temporal dynamics of habitats suitable for aquatic invertebrates. Flow in river bends is characterized by significant cross-stream velocities, which modify primary flow patterns, and create helical flow trajectories. Consequently, boundary shear stresses at the river-bed are altered, so that complex erosion, transport, and accumulation processes characteristically shape bed and bank morphology. The diversity of substrate types and complex bathymetry in meanders provide a large variety of habitat conditions for benthic invertebrates within a relatively small spatial domain, which are connected via hydraulic pathways. Periodic reversal of hydro-morphological processes between low and high flow, and seasonal growth of aquatic macrophytes creates spatio-temporal dynamics at the meso- and microhabitat scales. Such habitat dynamics increases benthic invertebrate diversity to the extent it is consistent with spatio-temporal scales of invertebrate mobility and life cycle. Furthermore, the presence of flow refugia, and hydraulic dead zones in meanders is essential to sustain species richness. This study concludes that meanders are highly complex morphodynamic elements that exhibit several self-regulating principles supporting invertebrate diversity and resilience in fluvial ecosystems.     

Species richness and trophic diversity increase decomposition in a co-evolved food web

Ecological communities show great variation in species richness, composition and food web structure across similar and diverse ecosystems. Knowledge of how this biodiversity relates to ecosystem functioning is important for understanding the maintenance of diversity and the potential effects of species losses and gains on ecosystems. While research often focuses on how variation in species richness influences ecosystem processes, assessing species richness in a food web context can provide further insight into the relationship between diversity and ecosystem functioning and elucidate potential mechanisms underpinning this relationship. Here, we assessed how species richness and trophic diversity affect decomposition rates in a complete aquatic food web: the five trophic level web that occurs within water-filled leaves of the northern pitcher plant, Sarracenia purpurea. We identified a trophic cascade in which top-predators--larvae of the pitcher-plant mosquito--indirectly increased bacterial decomposition by preying on bactivorous protozoa. Our data also revealed a facultative relationship in which larvae of the pitcher-plant midge increased bacterial decomposition by shredding detritus. These important interactions occur only in food webs with high trophic diversity, which in turn only occur in food webs with high species richness. We show that species richness and trophic diversity underlie strong linkages between food web structure and dynamics that influence ecosystem functioning. The importance of trophic diversity and species interactions in determining how biodiversity relates to ecosystem functioning suggests that simply focusing on species richness does not give a complete picture as to how ecosystems may change with the loss or gain of species.     

Monitoring change in aquatic invertebrate biodiversity: sample size, faunal elements and analytical methods

Replication is usually regarded as an integral part of biological sampling, yet the cost of extensive within-wetland replication prohibits its use in broad-scale monitoring of trends in aquatic invertebrate biodiversity. In this paper, we report results of testing an alternative protocol, whereby only two samples are collected from a wetland per monitoring event and then analysed using ordination to detect any changes in invertebrate biodiversity over time. Simulated data suggested ordination of combined data from the two samples would detect 20% species turnover and be a cost-effective method of monitoring changes in biodiversity, whereas power analyses showed about 10 samples were required to detect 20% change in species richness using ANOVA. Errors will be higher if years with extreme climatic events (e.g. drought), which often have dramatic short-term effects on invertebrate communities, are included in analyses. We also suggest that protocols for monitoring aquatic invertebrate biodiversity should include microinvertebrates. Almost half the species collected from the wetlands in this study were microinvertebrates and their biodiversity was poorly predicted by macroinvertebrate data.     

Use of the [14C]Leucine Incorporation Technique To Measure Bacterial Production in River Sediments and the Epiphyton

Bacterial production is a key parameter for the understanding of carbon cycling in aquatic ecosystems, yet it remains difficult to measure in many aquatic habitats. We therefore tested the applicability of the [¹⁴C]leucine incorporation technique for the measurement of bulk bacterial production in various habitats of a lowland river ecosystem. To evaluate the method, we determined (i) extraction efficiencies of bacterial protein from the sediments, (ii) substrate saturation of leucine in sediments, the biofilms on aquatic plants (epiphyton), and the pelagic zone, (iii) bacterial activities at different leucine concentrations, (iv) specificity of leucine uptake by bacteria, and (v) the effect of the incubation technique (perfused-core incubation versus slurry incubation) on leucine incorporation into protein. Bacterial protein was best extracted from sediments and precipitated by hot trichloroacetic acid treatment following ultrasonication. For epiphyton, an alkaline-extraction procedure was most efficient. Leucine incorporation saturation occurred at 1 μM in epiphyton and 100 nM in the pelagic zone. Saturation curves in sediments were difficult to model but showed the first level of leucine saturation at 50 μM. Increased uptake at higher leucine concentrations could be partly attributed to eukaryotes. Addition of micromolar concentrations of leucine did not enhance bacterial electron transport activity or DNA replication activity. Similar rates of leucine incorporation into protein calculated for whole sediment cores were observed after slurry and perfused-core incubations, but the rates exhibited strong vertical gradients after the core incubation. We conclude that the leucine incorporation method can measure bacterial production in a wide range of aquatic habitats, including fluvial sediments, if substrate saturation and isotope dilution are determined.     

Whole‐landscape modelling of compositional turnover in aquatic invertebrates informs conservation gap analysis: An example from south‐western Australia

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IRBAS: An online database to collate,analyze, and synthesize data on the biodiversity and ecology of intermittent rivers worldwide

Key questions dominating contemporary ecological research and management concern interactions between biodiversity, ecosystem processes, and ecosystem services provision in the face of global change. This is particularly salient for freshwater biodiversity and in the context of river drying and flow‐regime change. Rivers that stop flowing and dry, herein intermittent rivers, are globally prevalent and dynamic ecosystems on which the body of research is expanding rapidly, consistent with the era of big data. However, the data encapsulated by this work remain largely fragmented, limiting our ability to answer the key questions beyond a case‐by‐case basis. To this end, the Intermittent River Biodiversity Analysis and Synthesis (IRBAS; http://irbas.cesab.org ) project has collated, analyzed, and synthesized data from across the world on the biodiversity and environmental characteristics of intermittent rivers. The IRBAS database integrates and provides free access to these data, contributing to the growing, and global, knowledge base on these ubiquitous and important river systems, for both theoretical and applied advancement. The IRBAS database currently houses over 2000 data samples collected from six countries across three continents, primarily describing aquatic invertebrate taxa inhabiting intermittent rivers during flowing hydrological phases. As such, there is room to expand the biogeographic and taxonomic coverage, for example, through addition of data collected during nonflowing and dry hydrological phases. We encourage contributions and provide guidance on how to contribute and access data. Ultimately, the IRBAS database serves as a portal, storage, standardization, and discovery tool, enabling collation, synthesis, and analysis of data to elucidate patterns in river biodiversity and guide management. Contribution creates high visibility for datasets, facilitating collaboration. The IRBAS database will grow in content as the study of intermittent rivers continues and data retrieval will allow for networking, meta‐analyses, and testing of generalizations across multiple systems, regions, and taxa.     

Impact of three aquatic invasive species on native plants and macroinvertebrates in temperate ponds

Biological plant invasions pose a serious threat to native biodiversity and have received much attention, especially in terrestrial habitats. In freshwater ecosystems impacts of invasive plant species are less studied. We hypothesized an impact on organisms from the water column and from the sediment. We then assessed the impact of three aquatic invasive species on the plants and macroinvertebrates: Hydrocotyle ranunculoides, Ludwigia grandiflora and Myriophyllum aquaticum. Our research on 32 ponds in Belgium indicated that the reduction in the native plant species richness was a common pattern to invasion. However, the magnitude of impacts were species specific. A strong negative relationship to invasive species cover was found, with submerged vegetation the most vulnerable to the invasion. Invertebrate richness, diversity and abundance were measured in sediments of invaded and uninvaded ponds along a gradient of H. ranunculoides, L. grandiflora, and M. aquaticum species cover. We found a strong negative relationship between invasive species cover and invertebrate abundance, probably due to unsuitable conditions of the detritus for invertebrate colonization. Taxonomic compositions of aquatic invertebrate assemblages in invaded ponds differed from uninvaded ponds. Sensitive benthos, such as mayflies were completely absent in invaded ponds. The introduction of H. ranunculoides, L. grandiflora, and M. aquaticum in Belgian ponds has caused significant ecological alterations in the aquatic vegetation and the detritus community of ponds.     

Effects of soil and wood depletion on biodiversity

Human depletion of soil and wood resources is dramatically altering the biodiversity of both terrestrial and aquatic ecosystems. This paper provides an overview of the numerous linkages between the depletion of soil and wood resources and the loss of biodiversity. While some of these linkages are well documented, others remain speculative or unexplored. In order to understand the full ramifications of resource depletion on biodiversity, additional research is required.     

Microbial ecology and biodiversity in permafrost

Permafrost represents 26% of terrestrial soil ecosystems; yet its biology, essentially microbiology, remains relatively unexplored. The permafrost environment is considered extreme because indigenous microorganisms must survive prolonged exposure to subzero temperatures and background radiation for geological time scales in a habitat with low water activity and extremely low rates of nutrient and metabolite transfer. Yet considerable numbers and biodiversity of bacteria exist in permafrost, some of which may be among the most ancient viable life on Earth. This review describes the permafrost environment as a microbial habitat and reviews recent studies examining microbial biodiversity found in permafrost as well as microbial growth and activity at ambient in situ subzero temperatures. These investigations suggest that functional microbial ecosystems exist within the permafrost environment and may have important implications on global biogeochemical processes as well as the search for past or extant life in permafrost presumably present on Mars and other bodies in our solar system.