Interface Focus最新文献_第8页

Correction to: 'Current strategies with implementation of 3D cell culture: The challenge of quantification' (2022) by Temple et al. 对Temple等人的“目前实施3D细胞培养的策略:量化的挑战”(2022年)的更正。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0066

J Temple, E Velliou, M Shehata, R Lévy, P Gupta

引用次数: 0

Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors. 生物膜厚度控制着移动床生物膜反应器中微生物群落组装的随机和确定性过程的相对重要性。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0069

S Jane Fowler, Elena Torresi, Arnaud Dechesne, Barth F Smets

{"title":"Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors.","authors":"S Jane Fowler, Elena Torresi, Arnaud Dechesne, Barth F Smets","doi":"10.1098/rsfs.2022.0069","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0069","url":null,"abstract":"Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms of 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220069"},"PeriodicalIF":4.4,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9566247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Encounter rates prime interactions between microorganisms. 接触率决定了微生物之间的相互作用。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0059

Jonasz Słomka, Uria Alcolombri, Francesco Carrara, Riccardo Foffi, François J Peaudecerf, Matti Zbinden, Roman Stocker

{"title":"Encounter rates prime interactions between microorganisms.","authors":"Jonasz Słomka, Uria Alcolombri, Francesco Carrara, Riccardo Foffi, François J Peaudecerf, Matti Zbinden, Roman Stocker","doi":"10.1098/rsfs.2022.0059","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0059","url":null,"abstract":"Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell-cell or cell-resource encounters. Quantification and rational design of microbial interactions thus require quantification of encounter rates. Encounter rates can often be quantified through encounter kernels-mathematical formulae that capture the dependence of encounter rates on cell phenotypes, such as cell size, shape, density or motility, and environmental conditions, such as turbulence intensity or viscosity. While encounter kernels have been studied for over a century, they are often not sufficiently considered in descriptions of microbial populations. Furthermore, formulae for kernels are known only in a small number of canonical encounter scenarios. Yet, encounter kernels can guide experimental efforts to control microbial interactions by elucidating how encounter rates depend on key phenotypic and environmental variables. Encounter kernels also provide physically grounded estimates for parameters that are used in ecological models of microbial populations. We illustrate this encounter-oriented perspective on microbial interactions by reviewing traditional and recently identified kernels describing encounters between microorganisms and between microorganisms and resources in aquatic systems.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220059"},"PeriodicalIF":4.4,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10735036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The media composition as a crucial element in high-throughput metabolic network reconstruction. 介质组成是高通量代谢网络重建的关键因素。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-02-10 eCollection Date: 2023-04-06 DOI: 10.1098/rsfs.2022.0070

Benedict Borer, Stefanía Magnúsdóttir

{"title":"The media composition as a crucial element in high-throughput metabolic network reconstruction.","authors":"Benedict Borer, Stefanía Magnúsdóttir","doi":"10.1098/rsfs.2022.0070","DOIUrl":"10.1098/rsfs.2022.0070","url":null,"abstract":"In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the composition of the media (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates. We expand this analysis by using 106 MAGs from the same species with differing quality. We find that although the completeness of MAGs influences the fraction of gap-filled reactions, the composition of the media plays the dominant role in the accurate prediction of auxotrophies that form the basis of myriad community interactions. We propose that constraining the media composition for gap filling through both experimental approaches and computational approaches will increase the reliability of high-throughput reconstruction of genome-scale metabolic models from MAGs and paves the way for culture independent prediction of trophic interactions in complex microbial communities.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220070"},"PeriodicalIF":3.6,"publicationDate":"2023-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10735041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cultivating a more effective culture to advance the engineering of microbial communities 培养更有效的培养物以推进微生物群落工程

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-02-10 DOI: 10.1098/rsfs.2022.0073

S. J. Fowler, T. Curtis

引用次数: 1

Formation and emergent dynamics of spatially organized microbial systems. 空间组织微生物系统的形成和新兴动力学。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-02-10 eCollection Date: 2023-04-06 DOI: 10.1098/rsfs.2022.0062

Kelsey Cremin, Sarah J N Duxbury, Jerko Rosko, Orkun S Soyer

引用次数: 0

Correction to 'COVID-19: the case for aerosol transmission' 2022 by Tellier. 对泰利尔2022年《COVID-19:气溶胶传播的案例》的更正。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-02-06 DOI: 10.1098/rsfs.2022.0060

Raymond Tellier

引用次数: 0

Deriving calibrations for Arawakan using archaeological evidence. 利用考古证据得出阿拉瓦肯语的定标。

IF 3.6 3区生物学

Interface Focus Pub Date : 2022-12-09 eCollection Date: 2023-02-06 DOI: 10.1098/rsfs.2022.0049

Lev Michael, Fernando de Carvalho, Thiago Chacon, Konrad Rybka, Andrés Sabogal, Natalia Chousou-Polydouri, Gereon Kaiping

引用次数: 0

Multidisciplinary approaches to the Amazonian past: introduction to the theme issue 亚马逊过去的多学科研究方法:主题问题导论

IF 4.4 3区生物学

Interface Focus Pub Date : 2022-12-09 DOI: 10.1098/rsfs.2022.0068

Nicholas Q. Emlen, Leonardo Arias, Rik van Gijn

引用次数: 0

Diversity, multilingualism and inter-ethnic relations in the long-term history of the Upper Rio Negro region of the Amazon. 亚马逊上里奥内格罗地区长期历史中的多样性、多语言和种族间关系。

IF 3.6 3区生物学

Interface Focus Pub Date : 2022-12-09 eCollection Date: 2023-02-06 DOI: 10.1098/rsfs.2022.0050

Luis Cayón, Thiago Chacon

{"title":"Diversity, multilingualism and inter-ethnic relations in the long-term history of the Upper Rio Negro region of the Amazon.","authors":"Luis Cayón, Thiago Chacon","doi":"10.1098/rsfs.2022.0050","DOIUrl":"10.1098/rsfs.2022.0050","url":null,"abstract":"The Upper Rio Negro regional social system is made up of more than 30 languages belonging to six linguistic families. This results from socio-historical processes stretching back at least two millennia, which have built a system with different levels of autonomy and hierarchy associated with a mythical and ritual complex, and with social and linguistic exchanges. The analysis of these processes require an interdisciplinary outlook to understand the ways in which people from different linguistic families interacted and created it. More specifically, we ask how linguistic and cultural diversity have been created in the context of intense relations of multilingualism and inter-ethnic contact. To this end, we integrate perspectives from historical linguistics (regarding languages from the Tukanoan, Arawakan and Naduhup families) with archaeological data from the Amazonian past. Through this multidisciplinary approach, we seek to develop a linguistic-anthropological understanding of the dynamics shaping the region's diversity and inter-ethnic relations. We show that processes creating diversity are interrelated with changes in social histories, and are especially tied to the establishment of new forms of social organization as a result of pre-colonial inter-ethnic relations. This has led to the construction of various local multilingual ecologies connected to macro-regional processes in Amazonia.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 1","pages":"20220050"},"PeriodicalIF":3.6,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9732643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9116989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0