Struktura a funkce bakteriálních společenstev v průběhu sukcese na odumřelé rostlinné biomase

Rozklad odumřelé rostlinné biomasy se významnou měrou podílí na koloběhu uhlíku a je tak jedním z klíčových procesů probíhajících v lesích mírného pásu. Zatímco role hub při rozkladu opadu a dřeva byla opakovaně zkoumána, jen málo studií se zabývalo bakteriemi asociovanými s rozkládající se rostlinnou biomasou. Vývoj bakteriálního společenstva asociovaného se stromovým opadem je pravděpodobně způsoben změnami v chemickém složení opadu a dostupností živin. Aktivita hub značně přispívá ke změnám v substrátu a tím je ovlivněno také bakteriální společenstvo. Dostupnost živin se mění v průběhu rozkladu biomasy, na počátku jsou snadno dostupné lehce rozložitelné látky, zatímco později jsou rozkládány odolnější sloučeniny (např. lignin). Bakteriální kolonizace mrtvého dřeva je ovlivněna řadou faktorů, jako například místně specifické klimatické podmínky, druh stromu, objem dřeva. Cílem této práce bylo popsat dynamiku bakteriálního společenstva během dvouletého rozkladu stromového opadu a odumřelého dřeva. V opadovém experimentu bylo bakteriální společenstvo analyzováno v živých, odumírajících a rozkládajících se listech dubu zimního (Quercus petraea). Experiment probíhal v přírodní památce Xaverovský háj v České republice. Experiment s odumřelým dřevem byl zaměřen na složení bakteriálního společenstva v...The decomposition of dead plant biomass substantially contributes to the carbon cycle and therefore is one of the key processes in temperate forests. While the role of fungi in litter and deadwood decomposition was repeatedly addressed, there are just a few surveys of bacteria associated with decomposing plant biomass. The development of bacterial community within leaf litter is likely driven by the changes in litter chemistry and by the availability of nutrients in the litter. Fungal activity greatly contributes to changing properties of substrate and thus influences bacterial community. Availability of nutrients is changing during biomass decomposition from easily accessible substrates toward more recalcitrant ones (e.g. lignin). The colonization of deadwood by bacteria is influenced by various factors such as microclimate conditions, tree species and volume. The aim of this thesis was to describe bacterial community dynamics during the first two years of decomposition of leaf litter and deadwood. In the leaf litter experiment, bacterial community was analysed in the live, senescent and decomposing leaves of Quercus petraea. This experiment was performed in the Xaverovsky Haj Natural Reserve, Czech Republic. Deadwood experiment was focused on the composition of bacterial community in the initial...Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologiePřírodovědecká fakultaFaculty of Scienc

Bakterie asociované s rozkládajícím se dřevem

Odumřelé dřevo představuje významný habitat z hlediska biodiverzity a jeho rozklad v lesích mírného pásma přispívá k cyklům uhlíku a dusíku. Historicky doložený význam hub při rozkladu odumřelého dřeva byl v posledních letech doplněn o poznatky o roli bakterií v tomto procesu díky rychlému rozvoji metod založených na analýze nukleových kyselin. Pro studium procesu rozkladu dřeva byl vybrán smíšený temperátní les v Národní přírodní rezervaci Žofínský prales, ke kterému existuje bohatý historickým lesnický záznam o množství dřeva a kde rozklad odumřelého dřeva představuje důležitou součást celkového obratu rostlinné biomasy. Cílem této práce je detailně popsat roli bakterií v procesu rozkladu dřeva vzhledem ke složení bakteriálního společenstva, transkripce enzymů a metabolického potenciálu dominantních bakteriálních zástupců. Vliv stáří odumřelého dřeva spolu s pH a obsahem vody byl pro ovlivnění struktury bakteriálního společenstva důležitější než vliv druhu dřeva. Bakteriální společenstvo na počátku rozkladu se lišilo od pozdní fáze rozkladu. Složení houbového společenstva také významně ovlivňovalo složení bakterií. I přes přímý kontakt dřeva s půdou se bakterie a houby v těchto dvou habitatech lišily. Bakterie ve dřevě přispívaly k cyklu dusíku zejména fixací N2. Dále byly schopné využít uhlík...Deadwood is a hotspot of microbial diversity and its decomposition contributes to carbon and nitrogen cycling in temperate forests. The historically recognized importance of fungi in the decomposition of deadwood has recently been complemented by the description of bacterial functions thanks to the rapid progress of culture-independent methods based on the analysis of nucleic acids. To study different aspects of deadwood decomposition, a temperate mixed forest in Zofinsky prales National Nature Reserve was selected as a site with rich historical forestry data where deadwood decomposition represents an important process in wood turnover. The aim of this thesis is to describe role of bacteria in deadwood decomposition at fine scale resolution with respect to community composition, enzyme transcription, and metabolic potential of dominant species. Effects of deadwood age together with pH and water content on the bacterial community composition proved to be more important than tree species identity. Bacteria showed distinct composition between early and late community in decomposing deadwood. The bacterial community was also under a significant influence of fungal community composition. Despite being in a close contact, bacterial and fungal communities differed significantly between deadwood and the...Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologieFaculty of SciencePřírodovědecká fakult

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence

Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances.

Abstract: Background. Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data

Ecological roles of bacteria associated with plant litter

V lesích mírného pásu představuje rozklad stromového opadu významný přísun uhlíku do půdy. Hlavními hráči při dekompozici opadu jsou houby a bakterie. Zatímco role hub při rozkladu je často studována, jen málo prací se zabývá bakteriemi a jejich úlohou ve společenstvu opadu. Cílem této rešerše je shrnout dostupnou literaturu týkající se procesů a vztahů v bakteriálním společenstvu asociovaném s rostlinným opadem. Jsou diskutovány vlastnosti a charakter substrátů dostupných v rostlinné biomase. Zmíněny jsou směry výzkumu na úrovni genů pro různé enzymy. Do přehledu jsou dále zahrnuty faktory ovlivňující společenstvo, jako je diverzita, prostorové rozmístění a abiotické faktory. Lze předpokládat, že složení společenstva se vyvíjí se změnou chemismu opadu a dostupností živin. Tato dostupnost se v čase snižuje. Na začátku dekompozice jsou utilizovány jednoduché substráty, zatímco ty odolnější jsou rozkládány později za působení specializovaných skupin mikroorganizmů. Zdá se, že během rozkladu se uplatňují hlavně bakterie kmenů Actinobacteria, Acidobacteria, Bacteroidetes a Proteobacteria. Složení bakteriálního společenstva je také nejspíše ovlivňováno jeho interakcemi s houbami. Tato rešerše ukazuje, že bakteriální společenstvo asociované s rostlinným opadem je vysoce komplexní a dynamické díky kombinaci...Leaf litter in temperate forests represents an important input of carbon into the soil. Main players in the decomposition of leaf litter are fungi and bacteria. While the role of fungi in litter decomposition was repeatedly addressed, there are just a few field studies where litter-associated bacteria were also considered. The aim of this work was to summarize available literature studying the structure and function of bacterial community during litter degradation. The nature of different possible substrates is discussed. Genetic approach is briefly outlined. Factors such as diversity, spatially distribution and abiotic factors that can influence community are also considered. It can be supposed that community composition changes with the change of litter chemistry and nutrient availability. The development of bacterial community might be driven by the decreasing availability of nutrients in litter. Labile compounds are utilised at the beginning of decomposition, while recalcitrant substrates are utilised later by specialist taxa. Members of the phyla Actinobacteria, Acidobacteria, Bacteroidetes and Proteobacteria seem to be dominant during decomposition. Different types of relationships between fungi and bacteria also most likely influence the composition of community. This review shows that the bacterial...Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologieFaculty of SciencePřírodovědecká fakult

Structure and function of bacterial communities during succession on dead plant biomass

The decomposition of dead plant biomass substantially contributes to the carbon cycle and therefore is one of the key processes in temperate forests. While the role of fungi in litter and deadwood decomposition was repeatedly addressed, there are just a few surveys of bacteria associated with decomposing plant biomass. The development of bacterial community within leaf litter is likely driven by the changes in litter chemistry and by the availability of nutrients in the litter. Fungal activity greatly contributes to changing properties of substrate and thus influences bacterial community. Availability of nutrients is changing during biomass decomposition from easily accessible substrates toward more recalcitrant ones (e.g. lignin). The colonization of deadwood by bacteria is influenced by various factors such as microclimate conditions, tree species and volume. The aim of this thesis was to describe bacterial community dynamics during the first two years of decomposition of leaf litter and deadwood. In the leaf litter experiment, bacterial community was analysed in the live, senescent and decomposing leaves of Quercus petraea. This experiment was performed in the Xaverovsky Haj Natural Reserve, Czech Republic. Deadwood experiment was focused on the composition of bacterial community in the initial..

Bacteria associated with decomposing deadwood

Deadwood is a hotspot of microbial diversity and its decomposition contributes to carbon and nitrogen cycling in temperate forests. The historically recognized importance of fungi in the decomposition of deadwood has recently been complemented by the description of bacterial functions thanks to the rapid progress of culture-independent methods based on the analysis of nucleic acids. To study different aspects of deadwood decomposition, a temperate mixed forest in Zofinsky prales National Nature Reserve was selected as a site with rich historical forestry data where deadwood decomposition represents an important process in wood turnover. The aim of this thesis is to describe role of bacteria in deadwood decomposition at fine scale resolution with respect to community composition, enzyme transcription, and metabolic potential of dominant species. Effects of deadwood age together with pH and water content on the bacterial community composition proved to be more important than tree species identity. Bacteria showed distinct composition between early and late community in decomposing deadwood. The bacterial community was also under a significant influence of fungal community composition. Despite being in a close contact, bacterial and fungal communities differed significantly between deadwood and the..

Ecological roles of bacteria associated with plant litter

Leaf litter in temperate forests represents an important input of carbon into the soil. Main players in the decomposition of leaf litter are fungi and bacteria. While the role of fungi in litter decomposition was repeatedly addressed, there are just a few field studies where litter-associated bacteria were also considered. The aim of this work was to summarize available literature studying the structure and function of bacterial community during litter degradation. The nature of different possible substrates is discussed. Genetic approach is briefly outlined. Factors such as diversity, spatially distribution and abiotic factors that can influence community are also considered. It can be supposed that community composition changes with the change of litter chemistry and nutrient availability. The development of bacterial community might be driven by the decreasing availability of nutrients in litter. Labile compounds are utilised at the beginning of decomposition, while recalcitrant substrates are utilised later by specialist taxa. Members of the phyla Actinobacteria, Acidobacteria, Bacteroidetes and Proteobacteria seem to be dominant during decomposition. Different types of relationships between fungi and bacteria also most likely influence the composition of community. This review shows that the bacterial..