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Livestock production extension in Amazon has caused deforestation and soil degradation, with negative consequences on diversity and environmental services. Recently, rubber crops have been established in deteriorated soils of the Colombian Amazon as an option to restore hectares of unproductive degraded pastures. Bioindicator insects, such as termites, have been used to assess soil quality and fertility restoration. This study evaluated differences in termite abundance, species richness, and community composition in three different rubber crop systems as an indirect way of evaluating soil diversity restoring. Three rubber crop systems were sampled: clonal fields (rubber monocultures with different rubber clones), traditional commercial rubber plantations (rubber monocultures with just one rubber clone), and mixed plantations (rubber fields intercropped with copoazu fruit trees). Additionally, pastures in use for livestock production and natural forest relicts were compared to rubber crop systems, to serve as reference habitats. Termites were sampled using a 105-m transect method. Alpha diversity and beta diversity were estimated and compared between rubber crops and reference habitats. A total of 80 termite species belonging to two families were collected. Mixed plantations and pastures presented the lowest diversity rates. Species richness in rubber crop systems was 39% higher than that in pastures and included 72% of the termite species found in natural forests. Indicator species analysis associated soil-feeding termites with less diverse habitats and wood-feeding termites with high diverse habitats. Our results demonstrate that termite recovery will depend on the farming system selected and the agricultural practices implemented in the field, with some rubber crop systems, like commercial rubber plantations and clonal fields, recovering termite diversity better than others, such as mixed plantations.

Manioc (Manihot esculenta Crantz) is an important tropical crop that depends on arbuscular mycorrhizal (AM) association for its nutrition. However, little is known about the richness and species composition of AM fungal communities associating with manioc and possible differences across soils and manioc landraces. We studied the diversity and composition of AM fungal communities present in the roots of different manioc landraces and surrounding soils in indigenous shifting cultivation fields on different Amazonian soil types. A total of 126 AM fungal virtual taxa (VT; phylogenetically defined taxonomic units) were recovered from soil and root samples using 454 sequencing of AM fungal SSU rRNA gene amplicons. Different AM fungal communities occurred in different soil types. Minor differences occurred in the composition of AM fungal community associating with different manioc landraces, but AM fungal richness was not different among them. There was a low similarity between the AM fungal communities colonizing manioc roots and those recorded in the soil, independently of differences in soil properties or the manioc landrace evaluated. Rhizophagus manihotis and Glomus VT126 were the most abundant AM fungal species colonizing manioc roots. Contrasting with the results of earlier spore-based investigations, all the AM fungi identified as indicator species of particular manioc landraces were morphologically unknown Glomus species. In conclusion, different manioc landraces growing in common conditions associated with distinct AM fungal communities, whereby AM fungal communities in soils did not necessarily reflect the AM fungal communities colonizing manioc roots.

Rubber (Hevea brasiliensis, (Willd. Ex Adr. de Juss) Muell. Arg, Euphorbiaceae) is an important commercial latex-producing plant. Commercially, rubber is reproduced from a limited number of grifting genotypes. New promising genotypes have been selected to replace traditional genotypes. In addition, rubber has been promoted to recuperate Amazon soils degraded by extensive cattle ranching. Arbuscular mycorrhizal (AM) symbiosis is an important alternative for improving plant nutrition in rubber trees and recuperating degraded soils, but AM fungal communities on different plantations and in rubber genotypes are unknown. Spore abundance, root colonization and AM fungal community composition were evaluated in rubber roots of Colombian and introduced genotypes cultivated in degraded soils with different plantation types. Traditional (spore isolation and description, clearing and staining roots) and molecular techniques (Illumina sequencing) were used to assess AM fungi. Rubber roots hosted a diverse AM fungal community of 135 virtual taxa (VT) in 13 genera. The genus Glomus represented 66% of the total AM fungal community. Rubber genotype did not affect the arbuscular mycorrhization, hosting similar AM fungal communities. The composition of the AM fungal community on old and young rubber plantations was different. Diversity in AM fungi in rubber roots is an important characteristic for restoring degraded soils.

Livestock production extension in Amazon has caused deforestation and soil degradation, with negative consequences on diversity and environmental services. Recently, rubber crops have been established in deteriorated soils of the Colombian Amazon as an option to restore hectares of unproductive degraded pastures. Bioindicator insects, such as termites, have been used to assess soil quality and fertility restoration. This study evaluated differences in termite abundance, species richness, and community composition in three different rubber crop systems as an indirect way of evaluating soil diversity restoring. Three rubber crop systems were sampled: clonal fields (rubber monocultures with different rubber clones), traditional commercial rubber plantations (rubber monocultures with just one rubber clone), and mixed plantations (rubber fields intercropped with copoazú fruit trees). Additionally, pastures in use for livestock production and natural forest relicts were compared to rubber crop systems, to serve as reference habitats. Termites were sampled using a 105-m transect method. Alpha diversity and beta diversity were estimated and compared between rubber crops and reference habitats. A total of 80 termite species belonging to two families were collected. Mixed plantations and pastures presented the lowest diversity rates. Species richness in rubber crop systems was 39% higher than that in pastures and included 72% of the termite species found in natural forests. Indicator species analysis associated soil-feeding termites with less diverse habitats and wood-feeding termites with high diverse habitats. Our results demonstrate that termite recovery will depend on the farming system selected and the agricultural practices implemented in the field, with some rubber crop systems, like commercial rubber plantations and clonal fields, recovering termite diversity better than others, such as mixed plantations.

Made available in DSpace on 2021-06-25T11:52:41Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-04 European Regional Development Fund (Centre of Excellence EcolChange) University of Tartu (Estonian Research Council ) Moscow State University Natural Sciences and Engineering Research Council of Canada Discovery Grant Russian Science Foundation Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Swedish Research Council (Vetenskapsradet) The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide. Univ Tartu, Inst Ecol & Earth Sci, EE-51005 Tartu, Estonia Univ Manchester, Sch Earth & Environm Sci, Manchester M13 9PL, Lancs, England Qatar Univ, Environm Sci Ctr, Doha 2713, Qatar Moscow Lomonsov State Univ, Dept Ecol & Plant Geog, Fac Biol, Moscow 119991, Russia King Saud Univ, Zool Dept, Coll Sci, Riyadh 11451, Saudi Arabia Russian Acad Sci, Inst Biol Problems, North Far East Branch, Magadan 685000, Russia Swedish Univ Agr Sci, Dept Ecol, S-75651 Uppsala, Sweden Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada Univ Nacl Cordoba, Inst Multidisciplinario Biol Vegetal, CONICET, X5000HUA, Cordoba, Argentina Univ Nacl Rio Cuarto, Fac Agron & Vet, Dept Biol Agr, X5804BYA, Cordoba, Argentina Univ Penn, Dept Biol, Philadelphia, PA 19104 USA Russian Acad Sci, Inst Biol Problems Cryolithozone, Siberian Branch, Yakutsk 677000, Russia Univ Djibouti, Dept Rech Sci Environm, Private Bag 1904, Djibouti, Djibouti Univ Aveiro, Dept Biol, P-3810193 Aveiro, Portugal Univ Aveiro, CESAM, P-3810193 Aveiro, Portugal Thompson Rivers Univ, Dept Nat Resource Sci, Kamloops, BC V2C 0C8, Canada Jules Verne Univ Picardie, Ecol & Dynam Syst Anthropises, F-80037 Amiens, France Univ Namibia, Dept Wildlife Management & Ecotourism, Private Bag 1096, Katima Mulilo, Namibia RAS, FEB, Bot Garden Inst, Vladivostok 690024, Russia Univ Calif Riverside, Dept Microbiol & Plant Pathol, Riverside, CA 92521 USA Univ Western Ontario, Dept Biol, London, ON N6A 5B7, Canada UPR Forets & Societes, CIRAD, Yamoussoukro, Cote Ivoire Univ Montpellier, Forets & Societes, CIRAD, F-34000 Montpellier, France INP HB, Inst Natl Polytech Felix Houphouet Boigny, Yamoussoukro, Cote Ivoire Beni Suef Univ, Bot & Microbiol Dept, Fac Sci, Bani Suwayf 62511, Egypt Czech Acad Sci, Inst Microbiol, Prague 14220, Czech Republic Charles Univ Prague, Dept Expt Plant Biol, Fac Sci, Prague 12843, Czech Republic Estonian Univ Life Sci, Chair Biodivers & Nat Tourism, EE-51006 Tartu, Estonia Murdoch Univ, Harry Butler Inst, Iluka Chair Vegetat Sci & Biogeog, Perth, WA 6150, Australia Stellenbosch Univ, Dept Geog & Environm Studies, ZA-7602 Stellenbosch, South Africa Univ Rwanda, Sch Sci, Coll Sci & Technol, Kigali 3900, Rwanda Univ Bern, Inst Plant Sci, CH-3013 Bern, Switzerland Estonian Univ Life Sci, Chair Crop Sci & Plant Biol, EE-51006 Tartu, Estonia Botswana Int Univ Sci & Technol, Dept Biol Sci & Biotechnol, Private Bag 16, Palapye, Botswana Nakhon Phanom Univ, Dept Biol, Nakhon Phanom 48000, Thailand Univ Tartu, Nat Hist Museum, EE-51014 Tartu, Estonia Univ Palermo, Dept Agr Food & Forest Sci, I-90128 Palermo, Italy Univ Bangui, Ctr Studies & Res Pharmacopoeia & Tradit African, Bangui, Cent Afr Republ Inst Amazon Invest Cient Sinchi, Leticia 910001, Amazonas, Colombia Univ Estadual Paulista, Dept Biodivers, BR-13506900 Sao Paulo, Brazil Radboud Univ Nijmegen, Inst Water & Wetland Res, Dept Aquat Ecol & Environm Biol, NL-6525 AJ Nijmegen, Netherlands Univ Tartu, Dept Bot, EE-51005 Tartu, Estonia Univ Estadual Paulista, Dept Biodivers, BR-13506900 Sao Paulo, Brazil University of Tartu: PLTOM20903 (Estonian Research Council ): MOBTP 105 (Estonian Research Council ): MOBERC20 (Estonian Research Council ): PRG352 (Estonian Research Council ): PRG609 (Estonian Research Council ): PRG 1065 (Estonian Research Council ): PRG 1170 (Estonian Research Council ): PRG 1409 Moscow State University: AAAA-A16-116021660039-1 Russian Science Foundation: 19-14-00038 FAPESP: 2016/25197-0 Swedish Research Council (Vetenskapsradet): 2017-05019 Swedish Research Council (Vetenskapsradet): QUEX-CAS-QP-RD-18/19

Certain forestry and agricultural practices are known to affect arbuscular mycorrhizal (AM) fungal communities, but the effects of deforestation – including slash-and-burn management and other more severe disturbances – in tropical rain forests are poorly understood. We addressed the effects of anthropogenic disturbance on rain-forest AM fungal communities in French Guiana, by comparing mature tropical rain forest, slash-and-burn (5 y old) and clearcut areas (8 y old). A total of 36 soil samples were collected in six plots and sequenced using a high throughput 454-pyrosequencing platform. A total of 32649 sequences from 103 AM fungal virtual taxa (VT) were recorded. Whereas alpha diversity of AM fungi did not decrease due to land-use intensification, with average richness ranging from 17 to 21 taxa per plot, beta diversity (average distance to multivariate centroid) dropped by 28% from 0.46 in rain forest to 0.33 under clearcutting. AM fungal community composition was correlated with land use and soil chemical properties. Clearcut areas were characterized by the more frequent occurrence of specialist AM fungi, compared with mature forest or slash-and-burn areas. Specifically, clearcuts contained the highest proportions of VT that were geographic (21%), habitat (31%), abundance (97%) or host (97%) specialists based on VT metadata contained in the MaarjAM database. This suggests that certain AM fungi with narrow ecological niches have traits that allow them to exploit conditions of severe disturbance. In conclusion, slash-and-burn management appears to allow diverse AM fungal communities to persist, and may favour regeneration of tropical rain forest after abandonment. More severe disturbance in the form of clearcutting resulted in marked changes in AM fungal communities.

Amazonian rainforests once thought to hold an innate pristine wilderness, are increasingly known to have been densely inhabited by populations showing a diverse and complex cultural background prior to European arrival. To what extent these societies impacted their landscape is unclear. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies as a result of more sedentary habits. Much is known of the chemistry of these soils, yet their zoology, have been neglected. Hence, we characterised soil macroinvertebrate communities and activity in these soils at nine archaeological sites in three Amazonian regions. We found 667 morphospecies and a tenacious pre-Columbian footprint, with 43% of species found exclusively in ADEs. The soil biological activity is higher in the ADEs when compared to adjacent reference soils, and it is associated with higher biomass and richness of organisms known to engineer the ecosystem. We show that these habits have a unique pool of species, however, the contemporary land-use in ADEs drives nutrient decay and threats biodiversity. These findings support the idea that Humans have built and sustained a contrasting high fertile system that persisted until our days and irreversibly altered the biodiversity patterns in Amazonia.

Mycorrhizal associations are poorly studied in tropical environments, even in countries with tradition studying arbusclar and ecto-mycorrhizal associations. This chapter discusses advances and limitations on mycorrhizal associations in Colombia, including a case study of endo- and ecto-mycorrhizas in an Amazonian tropical rain forest. Most works about mycorrhizal associations in Colombia are limited to searching commercial-plants root colonization and quantifying arbuscular mycorrhizal fungal spores at soil (for arbuscular mycorrhizas), or searching fungal fruiting bodies near reported ectomycorrhizal plant species for inventories (for ectomycorrhizas). Few studies included mycorrhizal associations in natural ecosystems or the use of molecular tools. A case study showed that arbuscular mycorrhizal and ectomomycorrhizal fungi co-exist in tropical environments with similar fungal richness. The ecology and interactions of endo- and ecto-mycorrhizal fungi in this kind of tropical environments are still unknown and open new challenges for future research.

This paper presents an updated list of soil ants of the Colombian Amazon collected in three different river basins: the Amazon, the Caquetá and the Putumayo. The list includes 10 subfamilies, 60 genera and 218 species collected from TSBF monoliths at four different depths (Litter, 0 - 10 cm, 10 - 20 cm and 20 - 30 cm). This updated list increases considerably the knowledge of edaphic macrofauna of the region, due to the limited published information about soil ant diversity in the Colombian Amazon region.This is the first checklist of soil ant diversity of the Colombian Amazon region. Six new records of species for Colombia are exposed:Acropygatricuspis(LaPolla, 2004),Typhlomyrmexclavicornis(Emery, 1906),Typhlomyrmexmeire(Lacau, Villemant & Delabie, 2004),Cyphomyrmexbicornis(Forel, 1895),Megalomyrmexemeryi(Forel, 1904) andMyrmicocryptaspinosa(Weber, 1937), most of them corresponding to subterranean ants.

Amazonian indigenous people grow manioc in landscapes of different agricultural potential, yet studies on indigenous manioc production on fertile soils are scarce. Non-indigenous communities grow specific manioc landraces on fertile Amazonian Dark Earths (ADE), but it is unknown whether indigenous farmers also do so. During 2 years, we studied manioc cultivation by five indigenous groups on different Amazonian soils using quantitative and qualitative methods. We found that environmental conditions, including soil quality, are less important in determining manioc diversity and agricultural strategies than socioeconomic and socio-cultural factors such as labor availability, labor organization, and culinary preferences.

Outsiders often oversimplify Amazon soil use by assuming that abundantly available natural soils are poorly suited to agriculture and that sporadic anthropogenic soils are agriculturally productive. Local perceptions about the potentials and limitations of soils probably differ, but information on these perceptions is scarce. We therefore examined how four indigenous communities in the Middle Caqueta River region in the Colombian Amazon classify and use natural and anthropogenic soils. The study was framed in ethnopedology: local classifications, preferences, rankings, and soil uses were recorded through interviews and field observations. These communities recognized nine soils varying in suitability for agriculture. They identified anthropogenic soils as most suitable for agriculture, but only one group used them predominantly for their swiddens. As these communities did not perceive soil nutrient status as limiting, they did not base crop-site selection on soil fertility or on the interplay between soil quality and performance of manioc genetic resources.

Potentially nitrogen-fixing microaerobic and aerobic bacteria were isolated from several Colombian Amazon soils (forest, pastures and chagras) and two landscapes (floodable and non floodable areas). The abundance and distribution of bacteria were evaluated, as well as their relationship with soil physical and chemical characteristics. Landscape had a direct influence on the abundance of the microaerobic bacteria, with higher numbers in forest and pasture soils in non-floodable zones. The aerobic isolates (N=51) were grouped into 19 morphologies, with the highest numbers found in forest soil in floodable zones. A higher number of aerobic morphologies was shared among forest sites (Nonmetric Multidimensional Scaling and Analysis of Similarity p0.05), and 40% of the distribution was explained by lime percentage and Al concentration.

Understanding global biodiversity change, its drivers, and the ecosystem consequences requires a better appreciation of both the factors that shape soil macrofauna communities and the ecosystem effects of these organisms. The project ?sOilFauna? was funded by the synthesis center sDiv (Germany) to address this major gap by forming a community of soil ecologists, identifying the most pressing research questions and hypotheses, as well as conducting a series of workshops to foster the global synthesis and hypothesis testing of soil macrofauna. The overarching goal is to analyze the most comprehensive soil macrofauna database - the MACROFAUNA database - which collates abundance data of 17 soil invertebrate groups assessed with a standardized method at 7180 sites around the world, and seeks to foster the collection of future data. In a recent kick-off workshop in May 2022, the first research priorities and collaboration guidelines were determined. Here, we summarize the main outcomes of this workshop and highlight the benefits of creating an open global community of soil ecologists providing standardized soil macrofauna data for future research, evaluation of ecosystem health, and nature protection. Made available in DSpace on 2022-08-15T21:19:22Z (GMT). No. of bitstreams: 1 SoilOrganisms-2022-SoilFauna.pdf: 3420414 bytes, checksum: 086e310e9f8f7696a864d6c885d98df5 (MD5) Previous issue date: 2022 Workshop report.