Valentyna Krashevska

• Dr.
• PostDoc at Senckenberg Biodiversity and Climate Research Centre and LOEWE Centre for Translational Biodiversity Genomics

Cross‐kingdom associations play a fundamental role in ecological processes. Yet our understanding of plant–fungal co‐occurrences in tropical rainforests and the potential impacts of land‐use change shaping species connections remain limited. By using amplicon sequencing on DNA from roots and their associated fungal communities, we aim to understand...

Trophic interactions in micro‐food webs, such as those between nematodes and their bacterial prey, affect nitrogen cycling in soils, potentially changing nitrous oxide (N2O) production and consumption. However, how nematode‐mediated changes in soil bacterial community composition affect soil N2O emissions is largely unknown. Here, microcosm experim...

Soil biodiversity and the structure of soil animal communities are important foundations for forest ecosystem functions. Forest gap formation is an important forest management practice used to transform monocultures into mixed forests. However, whether and how gap size and age affect soil biodiversity and modify nematode communities remains limited...

The expansion of the oil palm industry in Indonesia has improved livelihoods in rural communities, but comes at the cost of biodiversity and ecosystem degradation. Here, we investigated ways to balance ecological and economic outcomes of oil palm cultivation. We compared a wide range of production systems, including smallholder plantations, industr...

Rainforest conversion and expansion of plantations in tropical regions change local microclimate and are associated with biodiversity decline. Tropical soils are a hotspot of animal biodiversity and may sensitively respond to microclimate changes, but these responses remain unexplored. To address this knowledge gap, here we investigated seasonal fl...

Introduction High-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databas...

Tropical soil microorganisms are major recyclers of the biosphere organic carbon. However, the link of tropical microorganisms to the two main pathways of how carbon enters the belowground system, i.e., plant roots and leaf litter, is poorly understood. To investigate the relative importance of these pathways, we studied the response of microorgani...

High-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delineating taxa, and downstream c...

Aim The diversity and distribution of soil microorganisms and their potential for long‐distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed thi...

The tropical Andes are a species-rich and nitrogen-limited system, susceptible to increased nitrogen (N) inputs from the atmosphere. However, our understanding of the impacts of increased N input on belowground systems, in particular on protists and their role in nutrient cycling, remains limited. We explored how increased N affects protists in tro...

Tropical soil microorganisms are major recyclers of biosphere organic carbon. However, the link of tropical microorganisms to the two primary carbon inputs (roots and litter) remains unclear. Here, we studied the effects of excluding living roots and litter on microorganisms in leaf litter and topsoil in rainforests and plantations in Sumatra, Indo...

In the United Nations Decade on Ecosystem Restoration¹, large knowledge gaps persist on how to increase biodiversity and ecosystem functioning in cash crop-dominated tropical landscapes². Here, we present findings from a large-scale, 5-year ecosystem restoration experiment in an oil palm landscape enriched with 52 tree islands, encompassing assessm...

Oil palm is the most productive oil crop, but its high productivity is associated with conventional management (that is, high fertilization rates and herbicide application), causing deleterious environmental impacts. Using a 2² factorial experiment, we assessed the effects of conventional vs reduced (equal to nutrients removed by fruit harvest) fer...

Paleoecological reconstructions of hydrological regimes in tropical peatlands during the Holocene are important for the estimation of their responses to changing environments. However, the application of some widely used proxies, such as testate amoebae, is hampered by poor knowledge of their morphology and ecological preferences in the region. The...

Global change is affecting soil biodiversity and functioning across all terrestrial ecosystems. Still, much is unknown about how soil biodiversity and function will change in the future in response to simultaneous alterations in climate and land use, as well as other environmental drivers. It is crucial to understand the direct, indirect and intera...

Deforestation and agricultural expansion in the tropics affect local and regional climatic conditions, leading to synergistic negative impacts on land ecosystems. Climatic changes manifest in increased inter‐ and intraseasonal variations and frequency of extreme climatic events (i.e., droughts and floods), which have evident consequences for aboveg...

Background Crop-tree thinning (CTT) is a forest management practice aiming at enhancing the growth of target trees in plantations by harvesting neighboring trees. Along with the positive effect on tree growth, thinning represents a disturbance, which likely affects belowground organisms and may feed back to stand productivity. However, the impact o...

Agricultural expansion is among the main threats to biodiversity and functions of tropical ecosystems. It has been shown that conversion of rainforest into plantations erodes biodiversity, but further consequences for food-web structure and energetics of belowground communities remains little explored. We used a unique combination of stable isotope...

Agricultural expansion is among the main threats to biodiversity and functions of tropical ecosystems. Conversion of rainforest into plantations erodes biodiversity with little-explored consequences for food-web structure and energetics of belowground communities, and associated ecosystem functions and services. We used a unique combination of appr...

Rainforest conversion and expansion of plantations in tropical regions are associated with changes in animal communities and biodiversity decline. In soil, Collembola are one of the most numerous invertebrate groups that affect the functioning of microbial communities and support arthropod predators. Despite that, information on the impact of chang...

In tropical forest ecosystems leaf litter from a large variety of species enters the de-composer system, however, the impact of leaf litter diversity on the abundance and activity of soil organisms during decomposition is little known. We investigated the effect of leaf litter diversity and identity on microbial functions and the abundance of micro...

Soils host most biodiversity on Earth, with a major fraction of its taxonomic diversity still to be uncovered and most of its functional knowledge to be determined. Much focus has been - and still is - on bacteria, fungi and animals. Clearly, without any of those components, soils would not function as they do. However, the group that constitutes t...

This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology...

Tropical peatlands play an important role in carbon storage and in water regulation on a landscape level. However, our understanding of their ecology and long-term hydrological dynamics remains limited. Transfer functions, constructed on the basis of biological indicators (proxies) with known ecological preferences, allow us to infer past environme...

Deforestation and land-use change in tropical regions result in habitat loss and extinction of species that are unable to adapt. The effects of tropical land-use change on ground spiders, a major group of invertebrate predators, are poorly known. With two methods, we showed >50% decline in spider density, species richness, functional diversity, and...

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional...

Land-use transitions can enhance the livelihoods of smallholder farmers but potential economic-ecological trade-offs remain poorly understood. Here, we present an interdisciplinary study of the environmental, social and economic consequences of land-use transitions in a tropical smallholder landscape on Sumatra, Indonesia. We find widespread biodiv...

Oil palm plantations are expanding rapidly throughout Southeast Asia due to increasing global food demand, thereby putting greater pressure on local ecosystems. These plantations usually replace rainforests, resulting in major losses of soil structure and fertility, and belowground biodiversity. However, despite causing soil degradation, oil palms...

Deforestation and land‐use change in tropical regions result in habitat loss and extinction of species that are unable to adapt to the conditions in agricultural landscapes. If the associated loss of functional diversity is not compensated by species colonizing the converted habitats, extinctions might be followed by a reduction or loss of ecosyste...

This chapter provides identification keys to free-living ciliates, amebida, and flagellated protozoa. Special detail is included for Ciliophora and Amoebida. Also, information on preparation methods, definition of the most relevant morphological terms, and current limitations in our knowledge of the group are provided. Additional information on the...

The diversity of naked amoebae and testate amoebae that inhabit the lentic and lotic ecosystems of the Neotropical region (from central Mexico and the Caribbean Islands, to the tip of South America) is discussed

Focusing on nematodes and their well-developed indices of community, ecosystem structure and function, we investigated the effects of the conversion of rainforest into rubber and oil palm plantations in Sumatra, Indonesia. Land use did not affect the total abundance of litter- and soil-dwelling nematodes, neither in riparian nor in well-drained sit...

Oil palm plantations are intensively managed agricultural systems that increasingly dominate certain tropical regions. Oil palm monocultures have been criticized because of their reduced biodiversity compared to the forests they historically replaced, and because of their negative impact on soils, water, and climate. We experimentally test whether...

Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 geore...

Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland r...

Microarthropods impact organic matter turnover and nutrient cycling via processing of organic matter entering the soil as litter and root exudates. Variations in the structure of soil microarthropod communities are due to both biotic and abiotic factors such as local climatic conditions and litter quality. However, in particular in tropical ecosyst...

Land-use intensification in the tropics plays an important role in meeting global demand for agricultural commodities but generates high environmental costs. Here, we synthesize the impacts of rainforest conversion to tree plantations of increasing management intensity on carbon stocks and dynamics. Rainforests in Sumatra converted to jungle rubber...

We investigated how the land-use change from rainforest into jungle rubber, intensive rubber and oil palm plantations affects decomposers and litter decomposition in Sumatra, Indonesia. Litterbags containing three litter types were placed into four land-use systems and harvested after 6 and 12 months. Litter mass loss and litter element concentrati...

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and othe...

We investigated the role of leaf litter chemistry and richness in affecting testate amoeba communities of tropical rainforest in the Ecuadorian Andes. Litterbags containing leaf litter from four dominating tree species (Clusia sp., Myrcia pubescens, Graffenrieda emarginata, and Cecropia andina) with richness 1, 2, and 4 species were established and...

Conversion of tropical rainforests into plantations fundamentally alters ecological niches of animal species. Generalist predators such as centipedes (Chilopoda) may be able to persist in converted ecosystems due to their ability to adapt and switch to alternative prey populations. We investigated variations in community composition and trophic nic...

Regression coefficients and coefficient of determination (R2) of body size—dry weight relationships in two centipede groups of different body shape. N, number of replicates; L, body length; W, body width. Regression coefficients apply to the relation y = a(x)b, where y is dry weight (mg) and x is body length (L), body length times body width (L x W...

Summary table from Canonical Correspondence Analysis (CCA) investigating environmental variables structuring centipede communities. Explanatory variables (S4 Table) account for 33.4% of the variation, adjusted explained variation is 13.1%. Permutation Test results: Axis 1 pseudo-F = 3.5, p = 0.108; Fall axes pseudo-F = 1.6, p = 0.03. (DOCX)

List of centipede species including full taxonomic name and authority, family affiliation, number of replicates (stable isotope ratios) and mean δ13C and δ15N values (± SD). Abbr., abbreviation used in figures. (DOCX)

Stable isotope values of litter material sampled in different conversion systems. Number of replicates and mean δ13C and δ15N values (± SD). (DOCX)

ANOVA results from generalized linear mixed effects models testing the effect of forest conversion on abundance, biomass and species richness of centipedes. Results are given for “intensity” models testing if conversion effects follow a linear trend from rainforest (F) to jungle rubber (J) to rubber (R) to oil palm plantations (O). Additionally, re...

Term effects of Canonical Correspondence Analysis (CCA) investigating correlations between abundances of centipede species and environmental variables. (DOCX)

Discriminant function analysis of centipede (Chilopoda) species in rainforests (F), jungle rubber (J), rubber (R) and oil palm (O). Range ellipses for the discriminants are given at the 95% confidence level. (DOCX)

Abundances (ind./m2) of centipede species on research plots representing four different rainforest conversion systems in two study regions. (DOCX)

Relationship of body cross sectional area (length x width) to dry weight in two centipede groups of different body shape. (a) Geophilomorpha, (b) Cryptopidae and Henicopidae. Data were log-transformed to reduce heteroscedasticity and to linearize the size-weight relationship. Regression equations are additionally given back transformed to the power...

Species accumulation curve showing the increase of centipede (Chilopoda) species with number of study sites. Means (' SD) based on 100 permutations. Dashed blue lines indicate bootstrap, first order jackknife and Chao extrapolations of the species pool in the study region [46]. (DOCX)

We investigated how altitude affects the decomposition of leaf and root litter in the Andean tropical montane rainforest of southern Ecuador, that is, through changes in the litter quality between altitudes or other site-specific differences in microenvironmental conditions. Leaf litter from three abundant tree species and roots of different diamet...

Here we describe the community structure of soil micro-invertebrates at three altitudes (1000, 2000, and 3000 m) and two soil layers (upper L/F layer and deeper H/Ah layer) of a tropical montane rainforest situated on the eastern slope of the Andes (southern Ecuador) with special focus on nematodes. Nematodes dominated the micro-invertebrate assemb...

Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quan-tification of land-use change and associated bundles of ec...

Primer pair sequences for plants, bacteria, and archaea

Supplementary Figures 1 - 9, Supplementary Tables 1 - 5, Supplementary Note 1 and Supplementary References

Large areas of tropical rainforest are being converted to agricultural and plantation land uses, but little is known of biodiversity and ecological functioning under these replacement land uses. We investigated the effects of conversion of rainforest into jungle rubber, intensive rubber and oil palm plantations on testate amoebae, diverse and funct...

Testate amoebae species list with mean density (a) and relative abundance (b) in the four land-use systems (F, rainforest; J, jungle rubber; R, rubber plantation; O, oil palm plantation) of the two localities studied (H, Harapan; B, Bukit Duabelas). (XLSX)

Characteristics of testate amoebae species (and abbreviations used in Fig 3) used for ascribing them to functional or trophic groups: shell composition, shell and aperture size, trophic level, sources for trophic level classification (see text for details). (XLSX)

Means and standard deviation of environmental factors used in the study. (XLSX)

Pearson correlations between environmental factors and density of testate amoebae species in litter and soil. (XLSX)

Tropical lowland rainforests are increasingly threatened by the expansion of agriculture and the extraction of natural resources. In Jambi Province, Indonesia, the interdisciplinary EFForTS project focuses on the ecological and socio-economic dimensions of rainforest conversion to jungle rubber agroforests and monoculture plantations of rubber and...

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities...

Archaeal OTU table at subplot level including taxonomic information.

Box plots of soil characteristics summarized by landscape and land use system.

Soil characteristics and georeferences of the analyzed plots.

Rarefaction analyses of the bacterial diversity of the two analyzed landscapes and four land use systems.

Observed bacterial OTUs and diversity at subplot level with summaries at plot level.

Bacterial OTU table at subplot level including taxonomic information.

Statistical analyses of soil characteristics.

Observed archaeal OTUs and diversity at subplot level with summaries at plot level.

Box plots of soil characteristics summarized by land use system.

Rarefaction analyses of the archaeal diversity of the two analyzed landscapes and four land use systems.