Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes

Barbi, Florian; Prudent, Elsa; Vallon, Laurent; Buée, Marc; Dubost, Audrey; Legout, Arnaud; Marmeisse, Roland; Fraissinet‐Tachet, Laurence; Luis, Patricia

doi:10.1016/j.soilbio.2016.06.008

Cited by 22 publications

(16 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in this work, no fungal indicator OTUs were specifically associated with A. marina or R. stylosa. The C/N ratio is known as factor that could influence forest fungal communities (Barbi et al, 2016) and contrasted values were reported in the present work, with an increase from the land-side to the sea-side, and an increase with depth. Indeed, Rhizophora sediments are known to be enriched in organic matter compared to Avicennia ones, notably because of a more extensive root system; these sediments are also more anoxic with a high sulphide content (Alongi et al, 2000;Marchand et al, 2004).…”

Section: The Influence Of Tree Species On Microbial Communities Compocontrasting

confidence: 89%

“…Moreover, Fungi tended to be tree-specific (Zhou and Hyde, 2001;Buée et al, 2011) even in the case of mangrove ecosystems where the aerial and intertidal parts of A. marina or R. stylosa exhibited different fungal communities (Arfi et al, 2012a). The C/N ratio is known as factor that could influence forest fungal communities (Barbi et al, 2016) and contrasted values were reported in the present work, with an increase from the land-side to the sea-side, and an increase with depth. The C/N ratio is known as factor that could influence forest fungal communities (Barbi et al, 2016) and contrasted values were reported in the present work, with an increase from the land-side to the sea-side, and an increase with depth.…”

Section: The Influence Of Tree Species On Microbial Communities Compocontrasting

confidence: 70%

See 1 more Smart Citation

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Luis

Saint-Genis

Vallon

et al. 2019

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

Summary Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non‐sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high‐throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.

show abstract

Section: The Influence Of Tree Species On Microbial Communities Compocontrasting

confidence: 89%

Section: The Influence Of Tree Species On Microbial Communities Compocontrasting

confidence: 70%

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Luis

Saint-Genis

Vallon

et al. 2019

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

show abstract

“…According to the holobiont hypothesis, the existence of plants in their environment requires a dedicated functional microbiome (Agler et al, 2016;Barbi et al, 2016;Sánchez-Cañizares, Jorrín, Poole, & Tkacz, 2017). In this context, the remarkable constancy of the trophic composition of the RAMs implies that temperate forests attract fungal assemblages that entail functional resilience under a certain range of climatic and edaphic conditions.…”

Section: The Dominance Of Mycorrhizal Fungi In Rams Of Fagaceae Andmentioning

confidence: 99%

Assembly processes of trophic guilds in the root mycobiome of temperate forests

et al. 2018

View full text Add to dashboard Cite

Root‐associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.

show abstract

“…As we predicted, the soil fungal communities were affected more strongly by tree species, whereas soil bacterial and archaeal communities were influenced more strongly by groundwater depth. Different plant species and their root exudates have been reported to affect soil microbial community and diversity [25,51,52]. Plant root exudates and soil organic matter content play an underappreciated role in shaping the soil fungal communities [25,26].…”

Section: Discussionmentioning

confidence: 99%

“…Plant root exudates and soil organic matter content play an underappreciated role in shaping the soil fungal communities [25,26]. It is demonstrated that beech and spruce trees species, with different litter quality, selected different soil fungal communities expressing different set of genes involved in organic matter degradation [52]. Another study indicated that 35%-37% of the dominant fungal "species" (operational taxonomic units, OTUs) were restricted to one or two tree species, whereas only about 15%-45% of fungal OTUs were common under six or seven tree species in the study [53], suggesting the significant effects of plant species on fungal community compositions.…”

Section: Discussionmentioning

confidence: 99%

Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

Gray

Gan

et al. 2020

Forests

View full text Add to dashboard Cite

Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.

show abstract

Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes

Cited by 22 publications

References 52 publications

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Assembly processes of trophic guilds in the root mycobiome of temperate forests

Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests

Contact Info

Product

Resources

About