Assessing Comparative Microbiome Performance in Plant Cell Wall Deconstruction Using Multi-omics-Informed Network Analysis

Plant cell walls are interwoven structures recalcitrant to degradation. Both native and adapted microbiomes are particularly effective at plant cell wall deconstruction. Studying these deconstructive microbiomes provides an opportunity to assess microbiome performance and relate it to specific microbial populations and enzymes. To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from time-dependent gene expression identified key deconstructive groups within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmanimonadetes populations. Functional analysis of gene expression demonstrated that the microbiomes proceeded through successional stages that are linked to enzymes that deconstruct plant cell wall polymers. This combination of network and functional analysis highlighted the importance of cellulose-active Actinobacteria in differentiating the performance of these microbiomes.

Successional and Intraspecific Variations in Leaf Traits, Spectral Reflectance Indices and Herbivory in a Brazilian Tropical Dry Forest

Leaf traits are good indicators of ecosystem functioning and can affect herbivory and leaf reflectance patterns, allowing a better understanding of changes in environmental conditions, such those observed during forest natural regeneration. The aim of this study was to evaluate the intraspecific variation in leaf traits and their influence on the pattern of herbivory and leaf reflectance in three species distributed along a successional gradient (early, intermediate and late stages) in a tropical dry forest (TDF) in northern Minas Gerais, Brazil. We sampled individuals of the following abundant tree species that occurred in multiple successional stages: Cenostigma pluviosum, Handroanthus ochraceus, and Tabebuia reticulata. We collected 10 leaves from each tree to determine the contents of chlorophyll a, b, and total, carotenoids and water, as well as the percentage of leaf area removed by herbivores and leaf specific mass (LSM). We also measured five spectral reflectance indices (Normalized Difference Vegetation Index-NDVI, Simple Ratio-SR, modified Normalized Difference-nND, modified SR-mSR and Water Index-WI) using a portable spectrometer. Our results showed intraspecific differences in most leaf traits along the successional gradient, suggesting that local adaptation may play an important role in plant community assembly. However, herbivory only differed for H. ochraceus in early and intermediate stages, but it was not affected by the leaf traits considered here. Spectral reflectance indices also differed among successional stage for all species together and for each species separately, except for T. reticulata in intermediate and late stages. Thus, leaf spectral signatures may be an important tool to the remote detection of different successional stages in TDFs, with implications for forest management.

Aboveground forest biomass varies across continents, ecological zones and successional stages: refined IPCC default values for tropical and subtropical forests

For monitoring and reporting forest carbon stocks and fluxes, many countries in the tropics and subtropics rely on default values of forest aboveground biomass (AGB) from the Intergovernmental Panel on Climate Change (IPCC) Guidelines for National Greenhouse Gas (GHG) Inventories. Default IPCC forest AGB values originated from 2006, and are relatively crude estimates of average values per continent and ecological zone. The 2006 default values were based on limited plot data available at the time, methods for their derivation were not fully clear, and no distinction between successional stages was made. As part of the 2019 Refinement to the 2006 IPCC Guidelines for GHG Inventories, we updated the default AGB values for tropical and subtropical forests based on AGB data from >25,000 plots in natural forests and a global AGB map where no plot data were available. We calculated refined AGB default values per continent, ecological zone, and successional stage, and provided a measure of uncertainty. AGB in tropical and subtropical forests varies by an order of magnitude across continents, ecological zones, and successional stage. Our refined default values generally reflect the climatic gradients in the tropics, with more AGB in wetter areas. AGB is generally higher in old-growth than in secondary forests, and higher in older secondary (regrowth >20 years old and degraded/logged forests) than in young secondary forests (≤20 years old). While refined default values for tropical old-growth forest are largely similar to the previous 2006 default values, the new default values are 4.0 to 7.7-fold lower for young secondary forests. Thus, the refined values will strongly alter estimated carbon stocks and fluxes, and emphasize the critical importance of old-growth forest conservation. We provide a reproducible approach to facilitate future refinements and encourage targeted efforts to establish permanent plots in areas with data gaps.

Successional Stages in Infant Gut Microbiota Maturation

After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influenced by many factors.

Bacterial and fungal communities experience rapid succession during the first year following a wildfire in a California chaparral.

The rise in wildfire frequency in the western United States has increased interest in secondary succession. However, despite the role of soil microbial communities in plant regeneration and establishment, microbial secondary succession is poorly understood owing to a lack of measurements immediately post-fire and at high temporal resolution. To fill this knowledge gap, we collected soils at 2 and 3 weeks and 1, 2, 3, 4, 6, 9, and 12 months after a chaparral wildfire in Southern California. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of the 16S and ITS2 amplicons. We found that fire severely reduced bacterial biomass by 47% and richness by 46%, but the impacts were stronger for fungi, with biomass decreasing by 86% and richness by 68%. These declines persisted for the entire post-fire year, but bacterial biomass and richness oscillated in response to precipitation, whereas fungal biomass and richness did not. Fungi and bacteria experienced rapid succession, with 5-6 compositional turnover periods. As with plants, fast-growing surviving microbes drove successional dynamics. For bacteria, succession was driven by the phyla Firmicutes and Proteobacteria, with the Proteobacteria Massilia dominating all successional time points, and the Firmicutes (Domibacillus and Paenibacillus) dominating early- to mid-successional stages (1-4.5 months), while the Proteobacteria Noviherbaspirillum dominated late successional stages (4.5-1 year). For fungi, succession was driven by the phyla Ascomycota, but ectomycorrhizal basidiomycetes, and the heat-resistant yeast, Geminibasidium were present in the early successional stages (1 month). However, pyrophilous filamentous Ascomycetes Pyronema, Penicillium, and Aspergillus, dominated all post-fire time points. While wildfires vastly decrease bacterial and fungal biomass and richness, similar to plants, pyrophilous bacteria and fungi increase in abundance and experience rapid succession and compositional turnover in the first post-fire year, with potential implications for post-fire chaparral regeneration

A preliminary investigation of the lichen biota associated with recently deglaciated terrain in southeastern Alaska

Glaciers worldwide are currently retreating at unprecedented rates, revealing large tracts of newly exposed rock and till. We present the results of a preliminary, qualitative investigation of the lichen diversity of transient habitats near three glaciers in southeastern Alaska: Muir Glacier within Glacier Bay National Park, and Baird and Patterson Glaciers in the Tongass National Forest. This work is noteworthy as it (i) documents previously undescribed lichen species and communities within rapidly changing glacier habitats, (ii) illustrates the importance of cryptogams (lichens, bryophytes, algae, and cyanobacteria) in the primary colonization of recently deglaciated terrain, (iii) sets apart the lichen biota of recently deglaciated terrain in southeastern Alaska from that of other glacial regions worldwide (e.g., the European Alps, Svalbard, and southern South America) and even other parts of Alaska (e.g., Brooks Range), and (iv) emphasizes the importance of more lichen studies that focus on this rapidly changing habitat. The lichen biotas found at different successional stages near these glaciers are described and compared. The role of lichens and other cryptogams in post-glacial vegetation initiation, the threats to the lichen biota, and suggestions for the possible origins of the lichen propagules that colonize these newly exposed surfaces are also discussed.

Soil Quality Restoration during the Natural Succession of Abandoned Cattle Pastures in Deforested Landscapes in the Colombian Amazon

Successional processes in abandoned pastures in the Amazon region have been well-documented for the floristic component; however, soil succession has been poorly studied. This study assessed the physical, chemical and biological responses of soils in the Amazon region during the natural succession process in two main landscapes of the Colombian Amazon. Soil data on soil physico–chemical (bulk density, macroaggregates, pH and minerals) and biological (soil macrofauna) composition were evaluated along chronosequence with four successional stages: (i) degraded pastures, (ii) young (10–20-year-old), (iii) middle-age (25–40-year-old) and (iv) mature forests, in two different landscapes (hill and mountain). Individual soil variables and a synthetic indicator of soil quality (GISQ) were evaluated as tools for natural succession monitoring. The results corroborated the negative impact that cattle ranching has on Amazon soils. After 10 years of natural succession, the physico–chemical and biological soil components were widely restored. Less soil compaction and organic carbon occurred in older successional stages. Soil macrofauna richness and density increased along the chronosequence, with an evident association between the macrofauna composition and the macroaggregates in the soil. None of the individual soil properties or the GISQ indicator discriminated among natural succession stages; therefore, new soil quality indicators should be developed to monitor soil quality restoration in natural successions.