Soil fungal community composition correlates with site-specific abiotic factors, tree community structure, and forest age in regenerating tropical rainforests

Simple Summary:& nbsp;Regenerating forests represent over half of all tropical forests. While regeneration processes of trees and animal groups have been studied, there is surprisingly little information about how the diversity and community composition of fungi and other microorganisms change and what ecological roles play in tropical forest regeneration. In this study, we compared the diversity and community composition of trees and soil fungi among primary forests and regenerating forests of different ages in two sampling areas in southern Costa Rica. Our study shows that while forest age has a significant influence, environmental factors, such as mesoclimate and soil chemistry, have stronger effects on both fungal and tree communities. Moreover, we observed that the more dissimilar tree communities are between any two sites, the more dissimilar the composition of fungal communities. The results presented here contribute to a better understanding of the successional processes of tropical forests in different regions and inform land use and forest management strategies, including, but not limited to, conservation, restoration, and sustainable use.Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data to compare richness and community composition along secondary forest succession in Costa Rica and assessed the potential roles of abiotic factors influencing them. We found a strong coupling of tree and soil fungal community structure in wet tropical primary and regenerating secondary forests. Forest age, edaphic variables, and regional differences in climatic conditions all had significant effects on tree and fungal richness and community composition in all functional groups. Furthermore, we observed larger site-to-site compositional differences and greater influence of edaphic and climatic factors in secondary than in primary forests. The results suggest greater environmental heterogeneity and greater stochasticity in community assembly in the early stages of secondary forest succession and a certain convergence on a set of taxa with a competitive advantage in the more persisting environmental conditions in old-growth forests. Our work provides unprecedented insights into the successional dynamics of fungal communities during secondary tropical forest succession.Plant science

Limited diagnostic accuracy and clinical impact of single-operator peroral cholangioscopy for indeterminate biliary strictures

BACKGROUND: Single-operator peroral cholangioscopy (sPOCS) is considered a valuable diagnostic modality for indeterminate biliary strictures. Nevertheless, studies show large variation in its characteristics and measures of diagnostic accuracy. Our aim was to estimate the diagnostic accuracy of sPOCS visual assessment and targeted biopsies for indeterminate biliary strictures. Additional aims were: estimation of the clinical impact of sPOCS and comparison of diagnostic accuracy with brush cytology. METHODS: A retrospective single-center study of adult patients who underwent sPOCS for indeterminate biliary strictures was performed. Diagnostic accuracy was defined as sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The clinical impact of sPOCS was assessed by review of medical records, and classified according to its influence on patient management. RESULTS: 80 patients were included, with 40 % having primary sclerosing cholangitis (PSC). Prior ERCP was performed in 88 %, with removal of a biliary stent prior to sPOCS in 55 %. The sensitivity, specificity, PPV, and NPV for sPOCS visual impression and targeted biopsies were 64 %, 62 %, 41 %, and 84 %, and 15 %, 65 %, 75 %, and 69 %, respectively. The clinical impact of sPOCS was limited; outcome changed management in 17 % of patients. Sequential brush cytology sensitivity, specificity, PPV, and NPV were 47 %, 95 %, 80 %, and 83 %. CONCLUSIONS: The diagnostic accuracy of sPOCS for indeterminate biliary strictures was found to be inferior to brush cytology, with a low impact on patient management. These findings are obtained from a select patient population with a high prevalence of PSC and plastic stents in situ prior to sPOCS

MADERA: A standardized Pan-Amazonian dataset for tropical timber species

We compiled and presented a dataset for all timber species reported in the Amazon region from all nine South American Amazonian countries. This was based on official information from every country, as well as from two substantial scientific references. We verified the standard taxonomic names from each individual source, using the Taxonomic Name Resolution Service (TNRS) and considered all Amazonian tree species with diameter at breast height (DBH) ≥10 cm. We also obtained estimates of the current population size for most species from a published approach based on data from 1900 tree inventory plots (1-ha each) distributed across the Amazon region and part from the Amazon Tree Diversity Network (ATDN). We then identified the hyperdominant timber species. In addition, we overlapped our timber species list with data for species that are used for commercial purposes, according to the International Tropical Timber Organization (ITTO), the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the International Union for Conservation of Nature (IUCN) taxa assessment and Red List categories. Finally, we also included IUCN Red List categories based on combined deforestation, and climate change scenarios for these species. Our final Amazonian timber species dataset contains 1112 unique species records, which belong to 337 genera and 72 families from the lowland Amazonian rainforest, with associated information related to population, conservation, and trade status of each species. The authors of this research expect that the information provided will be useful to strengthen the public forestry policies of the Amazon countries, inform ecological studies, as well for forest management purposes. The data are released under the Creative Commons Attribution 4.0 International license

Modelling the distribution of Amazonian tree species in response to long-term climate change during the mid-late Holocene

Aim To (a) assess the environmental suitability for rainforest tree species of Moraceae and Urticaceae across Amazonia during the Mid‐Late Holocene and (b) determine the extent to which their distributions increased in response to long‐term climate change over this period. Location Amazonia. Taxon Tree species of Moraceae and Urticaceae. Methods We used MaxEnt and inverse distance weighting interpolation to produce environmental suitability and relative abundance models at 0.5‐degree resolution for tree species of Moraceae and Urticaceae, based on natural history collections and a large plot dataset. To test the response of the Amazon rainforest to long‐term climate change, we quantified the increase in environmental suitability and modelled species richness for both families since the Mid‐Holocene (past 6,000 years). To test the correlation between the relative abundance of these species in modern vegetation versus modern pollen assemblages, we analysed the surface pollen spectra from 46 previously published paleoecological sites. Results We found that the mean environmental suitability in Amazonia for species of Moraceae and Urticaceae showed a slight increase (6.5%) over the past 6,000 years, although southern ecotonal Amazonia and the Guiana Shield showed much higher increases (up to 68%). The accompanied modelled mean species richness increased by as much as 120% throughout Amazonia. The mean relative abundance of Moraceae and Urticaceae correlated significantly with the modern pollen assemblages for these families. Main Conclusions Increasing precipitation between the Mid‐ and Late Holocene expanded suitable environmental conditions for Amazonian humid rainforest tree species of Moraceae and Urticaceae, leading to rainforest expansion in ecotonal areas of Amazonia, consistent with previously published fossil pollen data

The ghosts of forests past and future : deforestation and botanical sampling in the Brazilian Amazon

The remarkable biodiversity of the Brazilian Amazon is poorly documented and threatened by deforestation. When undocumented areas become deforested, in addition to losing the fauna and flora, we lose the opportunity to know which unique species had occupied a habitat. Here we quantify such knowledge loss by calculating how much of the Brazilian Amazon has been deforested and will likely be deforested until 2050 without having its tree flora sufficiently documented. To this end, we analysed 399 147 digital specimens of nearly 6000 tree species in relation to official deforestation statistics and future deforestation scenarios. We find that by 2017, 30% of all the localities where tree specimens had been collected were mostly deforested. Some 300 000 km(2)(12%; 485 25 x 25 km grid cells) of the Brazilian Amazon had been deforested by 2017, without having a single tree specimen recorded. An additional 250 000-900 000 km(2)of severely under-collected rainforest will likely become deforested by 2050. If future tree sampling is to cover this area, sampling effort has to increase two- to six-fold. Nearly 255 000 km(2)or 7% of rainforest in the Brazilian Amazon is easily accessible but does yet but remain under-collected. Our study highlights how progressing deforestation increases the risk of losing undocumented species of a hyper-diverse tree flora.Peer reviewe