Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene

Backgroud

Foliicolous algae are a common occurrence in tropical forests. They are referable to a few simple morphotypes (unicellular, sarcinoid-like or filamentous), which makes their morphology of limited usefulness for taxonomic studies and species diversity assessments. The relationship between algal community and their host phyllosphere was not clear. In order to obtain a more accurate assessment, we used single molecule real-time sequencing of the 18S rDNA gene to characterize the eukaryotic algal community in an area of South-western China.

Result

We annotated 2922 OTUs belonging to five classes, Ulvophyceae, Trebouxiophyceae, Chlorophyceae, Dinophyceae and Eustigmatophyceae. Novel clades formed by large numbers sequences of green algae were detected in the order Trentepohliales (Ulvophyceae) and the Watanabea clade (Trebouxiophyceae), suggesting that these foliicolous communities may be substantially more diverse than so far appreciated and require further research. Species in Trentepohliales, Watanabea clade and Apatococcus clade were detected as the core members in the phyllosphere community studied. Communities from different host trees and sampling sites were not significantly different in terms of OTUs composition. However, the communities of Musa and Ravenala differed from other host plants significantly at the genus level, since they were dominated by Trebouxiophycean epiphytes.

Conclusion

The cryptic diversity of eukaryotic algae especially Chlorophytes in tropical phyllosphere is very high. The community structure at species-level has no significant relationship either with host phyllosphere or locations. The core algal community in tropical phyllopshere is consisted of members from Trentepohliales, Watanabea clade and Apatococcus clade. Our study provided a large amount of novel 18S rDNA sequences that will be useful to unravel the cryptic diversity of phyllosphere eukaryotic algae and for comparisons with similar future studies on this type of communities.

     

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)

Microorganisms of plant phyllosphere play an important role in plant health and productivity and are influenced by abiotic and biotic factors. In this study, we investigated the phyllosphere bacterial communities of three cigar tobacco varieties cultivated in Guangcun (GC) and Wuzhishan (WZS), Hainan, China. Metagenomic DNA was extracted from tobacco leaf samples and sequenced by 16S rDNA amplicon sequencing. Our results showed that bacterial communities of cigar tobacco phyllosphere in GC exhibited remarkably higher alpha diversity than that in WZS. There was slight effect of tobacco genotype variations on the alpha diversity in both cultivation sites, and beta diversity and structure of bacterial community were not influenced significantly by the cultivation sites and tobacco varieties. Statistical analyses of species diversity unraveled that the dominant species in bacterial communities of cigar tobacco phyllosphere among all these samples were phylogenetically affiliated to Proteobacteria and Cyanobacteria. At the genus level, the most abundant microorganism was Limnobacter, followed by Brevundimonas, unidentified_Cyanobacteria, and Pseudomonas. Additionally, environmental conditions except for humidity were negatively correlated with the relative abundance of bacterial genera. Further analyses revealed that influence of site‐specific factors on tobacco bacterial community was relatively higher than genotype‐specific factors. In short, this study may contribute to the knowledge base of practical applications of bacterial inoculants for tobacco leaf production.     

Diversity of subaerial algae and cyanobacteria on tree bark in tropical mountain habitats

We report the species composition of subaerial epixylic algae and cyanobacteria from a South-East Asian mountain rainforest locality in Cibodas, West Java. Green algae (Trebouxiophyceae, Chlorophyceae, Trentepohliales) were dominant and Cyanobacteria were the second most frequent group. We specifically concentrated on the comparison of species composition of closed primary forest and open antropogenic spaces. Trentepohliales and Cyanobacteria dominated in open spaces with higher light intensities, whereas closed forest localities were dominated by trebouxiophycean coccal green algae. There was a significantly higher algal diversity in open spaces than in closed forest samples indicating the limiting effect of light on subaerial algal communities of closed tropical forests. A number of isolated strains and morphotypes probably represent undescribed taxa. Presented at the International Symposium Biology and Taxonomy of Green Algae V, Smolenice, June 26–29, 2007, Slovakia.     

Butterfly community recovery in degraded rainforest habitats in the Upper Guinean Forest Zone (Kakum forest, Ghana)

Successful regeneration of secondary tropical forest might be crucial in the conservation of rainforests, since large areas of primary forest have been destroyed or degraded. Animal communities might play an important role in restoration of biological diversity in these secondary habitats, since some groups have high mobility and capacity for dispersal. Fruit-feeding butterflies were trapped to measure differences between butterfly communities in primary rainforest and disturbed forest habitats of different stage of regeneration including clear-cut, abandoned farmland, newly planted forest and middle-aged secondary growth. 3465 specimens representing 114 species were identified from 56 traps operated for 36 days. Extremely high values of rarefied species richness were estimated in the clear-cut habitat, due to the high number of singletons and doubletons. This was caused by a gap-effect that allowed penetration of canopy and open area species after disturbance. The differences between butterfly communities were best demonstrated through ecological composition, richness and abundance of indicator groups and habitat similarity based on Jaccard’s similarity index. The results show a clear ability of butterfly communities in degraded forest habitats to regenerate in 50–60 years after clearance.     

Disentangling the roles of spatial and environmental variables in shaping benthic algal assemblages in rivers of central and northern China

Benthic algae were collected from central and northern Chinese rivers to test the hypothesis that geographic location has significant contributions in shaping algal assemblages. We used Moran’s eigenvector maps (MEM) to model spatial components and variation partitioning to quantify the influences of spatial and environmental variables on regional patterns of algal richness and community composition, respectively. We found that variation in algal richness was attributed to MEM component 2, 8, and 9 and the quadratic term of N–NO₃. Regarding abundance data, latitude, longitude, and MEM component 1, 2, and 7 were important spatial variables. Although P–PO₄, pH, and annual mean temperature were significant environmental variables influencing algal community composition, they were all spatially structured. Among the total explained variance in both algal metrics, spatial proportions were higher than that of environmental variables. We also found that abundant species of Achnanthidium minutissimum, Cocconeis placentula, Cymbella delicatula, Cymbella affinis, Cymbella turgidula, and Synedra ulna displayed clear spatially related patterns. In conclusion, the contributions of spatial and environmental variables to regional variation of algal assemblages are scale-dependent. As for our study scale (~1,000 km), spatial control may be more important. Since spatial effects could obscure local environmental impacts on algal communities, appropriate study scale and statistical methods should be taken into account in algal bioassessment. We recommend inclusion of both algal richness and community composition in study of algal biogeography, due to their different relationships with spatial and environmental variables.     

High Diversity Revealed in Leaf‐Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf‐inhabiting microorganisms, recently termed “phyllosphere microbiome”. Microbial prey, however, attract microbial predators. Protists in particular have been shown to structure bacterial communities on plant surfaces, but virtually nothing is known about the community composition of protists on leaves. Using newly designed specific primers targeting the 18S rDNA gene of Cercozoa, we investigated the species richness of this common protist group on leaves of four Brassicaceae species from two different locations in a cloning‐based approach. The generated sequences revealed a broad diversity of leaf‐associated Cercozoa, mostly bacterial feeders, but also including known plant pathogens and a taxon of potential endophytes that were recently described as algal predators in freshwater systems. This initial study shows that protists must be regarded as an integral part of the microbial diversity in the phyllosphere of plants.     

Richness and Composition of Ground-dwelling Ants in Tropical Rainforest and Surrounding Landscapes in the Colombian Inter-Andean Valley

Tropical rainforests are characterized by having high structural complexity, stratification, and species diversity. In Colombia, tropical rainforests are critically endangered with only 24% of their area remaining. Forest fragments are often valued based on the presence of vertebrate taxa despite that small habitat remnants may still harbor diverse invertebrate communities. We surveyed the ant fauna associated with rainforest fragments and their surrounding landscape elements (including mature forests, flooded forests, gallery forests, live fences, and pastures) in the Magdalena River watershed. Pitfall traps and litter samples were used to estimate ant richness and diversity, and to compare ant composition among landscape elements. We found 135 species from 42 genera, representing 16% of the species and 43% of the genera known for Colombia. Our surveys also uncovered 11 new ant records for the Colombian inter-Andean region and 2 new records for the country of Colombia: Mycocepurus curvispinosus (Mackay) and Rhopalothrix isthmica (Weber). The highest species richness was found in forest-covered sites, and richness and diversity was lower in the disturbed landscapes surrounding the forest patches. Species composition varied significantly between all habitat types, but was most similar between forest types suggesting that a loss of structural complexity has the greatest effect on ant communities. Across our study sites, ten species showed the greatest response to habitat type and could qualify as indicator taxa for this region. We conclude by discussing the value of conserving even small forests in this landscape due to their ability to retain high diversity of ants.     

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.     

Community level physiological study of algicidal bacteria in the phycospheres of Skeletonema costatum and Scrippsiella trochoidea

Bacteria in the phycosphere have a unique ecological relationship with host algae due to their utilization of algal extracellular products as nutrients. Some bacteria control the growth of algal cells and even lyse them. The diversity of bacteria and their community dynamics in the phycosphere of microalgae are still relatively little understood, especially of those associated with red tide-causing algae. In this study, scanning electron microscope (SEM) images of algal cell morphology revealed that the phycosphere bacteria of the red tide-causing algae, Skeletonema costatum and Scrippsiella trochoidea, could lyse them within 72 h. The community level physiology of the algicidal bacteria was studied using Biolog ECO microplates, a common method for the ecological study of microbial communities. The average well color development (AWCD) values of bacteria in the phycospheres of both species were low, indicating that the bacteria had low metabolic activity overall. The diversity indices were both lower than the bacterial diversity from natural environments. However, the bacteria associated with S. trochoidea demonstrated a higher AWCD value and diversity than those in the phycosphere of S. costatum. The utilization of carbon sources significantly changed at different lytic times, reflecting that the bacterial community structure changed during the algae-lysing process. These results revealed that the bacterial communities in phycospheres had a simple structure and low diversity. When the balance between algae and bacteria broke down, the total bacterial density increased while the algicidal bacteria accumulated and became the dominant species, changing the bacterial community structure in this micro-ecosystem.     

Bacterial Community Assemblages Associated with the Phyllosphere,Dermosphere, and Rhizosphere of Tree Species of the Atlantic Forest are Host Taxon Dependent

Bacterial communities associated with tree canopies have been shown to be specific to their plant hosts, suggesting that plant species-specific traits may drive the selection of microbial species that comprise their microbiomes. To further examine the degree to which the plant taxa drive the assemblage of bacterial communities in specific plant microenvironments, we evaluated bacterial community structures associated with the phyllosphere, dermosphere, and rhizosphere of seven tree species representing three orders, four families and four genera of plants from a pristine Dense Ombrophilous Atlantic forest in Brazil, using a combination of PCR-DGGE of 16S rRNA genes and clone library sequencing. Results indicated that each plant species selected for distinct bacterial communities in the phyllosphere, dermosphere, and rhizosphere, and that the bacterial community structures are significantly related to the plant taxa, at the species, family, and order levels. Further characterization of the bacterial communities of the phyllosphere and dermosphere of the tree species showed that they were inhabited predominantly by species of Gammaproteobacteria, mostly related to Pseudomonas. In contrast, the rhizosphere bacterial communities showed greater species richness and evenness, and higher frequencies of Alphaproteobacteria and Acidobacteria Gp1. With individual tree species each selecting for their specific microbiomes, these findings greatly increase our estimates of the bacterial species richness in tropical forests and provoke questions concerning the ecological functions of the microbial communities that exist on different plant parts.     

Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant–fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.     

Butterfly species and traits associated with selectively logged forest in Borneo

Logging can significantly change the structure of rainforest communities. To better understand how logging drives this change, butterflies and environmental variables were assessed within both unlogged and logged forest in Indonesian Borneo. In the whole dataset, we found local environmental variables and geographic distance combined captured 53.1% of the variation in butterfly community composition; 29.6% was associated with measured local environmental variables, 13.6% with geographic distance between sites, and 9.9% with covariation between geographic distance and environmental variables. The primary axis of variation in butterfly community composition represented a disturbance gradient from unlogged to logged forest. Subsequent axes represented gradients influenced by variables such as canopy cover and total tree density. There were significant associations between environmental variables and geographic range and larval host plant use of species. Specifically, butterflies using trees as larval host plants and those with distributions limited to Borneo were more likely to be present in unlogged forest. By contrast, species that tended to be more abundant in logged forest were those with widespread distributions and those using lianas and grasses as larval host plants. The results of this study highlight the importance of environmental variables and disturbance, e.g., selective logging, in structuring rainforest community diversity. Moreover, they confirm how species traits, such as larval food use and geographic distributions can determine patterns of species abundance following environmental change.     

Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.     

长白山溪流河岸带森林木本植物多样性沿海拔梯度分布规律

采用样带网格调查方法和α、β多样性指数分析方法,研究了长白山河岸带原始林和次生林群落木本植物多样性沿海拔梯度分布规律及其对采伐干扰的响应.结果表明：不同海拔区域河岸带原始林群落均由11～13个树种组成,其在群落中的地位随海拔升高而发生变化,阔叶树种优势地位逐步被针叶树种所取代,采伐干扰不仅改变了群落树种丰富度及其在群落中的地位,而且使针叶树种取代阔叶树种的趋势有所增强;河岸带原始林群落物种多样性沿海拔梯度呈现出中、低海拔区域相对较高且比较恒定(2.454～2.544),高海拔区域(2.250)下降的分布规律,采伐干扰改变了其沿海拔梯度分布格局(波动型),加大了不同海拔区域群落间的波动性(2.174～2.692);河岸带原始林群落树种沿海拔梯度的变动速率相对较低(1.5～3.5),且群落相似性较高(0.85～0.94),采伐干扰使次生林群落树种沿海拔梯度的变动幅度增大(0.5～6.0),群落相似性下降(0.68～0.91),但次生林群落沿海拔梯度分布仍具有较高连续性.     

Arbuscular mycorrhizal fungal communities along a pedo-hydrological gradient in a Central Amazonian terra firme forest

Little attention has been paid to plant mutualistic interactions in the Amazon rainforest, and the general pattern of occurrence and diversity of arbuscular mycorrhizal fungi (AMF) in these ecosystems is largely unknown. This study investigated AMF communities through their spores in soil in a ‘terra firme forest’ in Central Amazonia. The contribution played by abiotic factors and plant host species identity in regulating the composition, abundance and diversity of such communities along a topographic gradient with different soils and hydrology was also evaluated. Forty-one spore morphotypes were observed with species belonging to the genera Glomus and Acaulospora, representing 44 % of the total taxa. Soil texture and moisture, together with host identity, were predominant factors responsible for shaping AMF communities along the pedo-hydrological gradient. However, the variability within AMF communities was largely associated with shifts in the relative abundance of spores rather than changes in species composition, confirming that common AMF species are widely distributed in plant communities and all plants recruited into the forest are likely to be exposed to the dominant sporulating AMF species.     

Surprising low diversity of the plant pathogen Phytophthora in Amazonian forests

The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them cause the collar and root-rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in the Neotropical forests where natural enemies could maintain the huge plant diversity via negative density dependence. We characterized the diversity of soil-borne Phytophthora communities in the North French Guiana rainforest and investigated how they are structured by host identity and environmental factors. In this little-explored habitat, 250 soil cores were sampled from 10 plots hosting 10 different plant families across three forest environments (Terra Firme, Seasonally Flooded and White Sand). Phytophthora diversity was studied using a baiting approach and metabarcoding (High-Throughput Sequencing) on environmental DNA extracted from both soil samples and baiting-leaves. These three approaches revealed very similar communities, characterized by an unexpected low diversity of Phytophthora species, with the dominance of two cryptic species close to Phytophthora heveae. As expected, the Phytophthora community composition of the French Guiana rainforest was significantly impacted by the host plant family and environment. However, these plant pathogen communities are very small and are dominated by generalist species, questioning their potential roles as drivers of plant diversity in these Amazonian forests.     

Distinctive Phyllosphere Bacterial Communities in Tropical Trees

Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of ‘true’ tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1–V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1–6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.     

西双版纳热带植物园蝴蝶的多样性及变化

中国科学院西双版纳热带植物园（简称“版纳植物园”）保存着上万种植物,且生境多样,具有较高的蝴蝶多样性。本研究选择三类代表性生境：片段化雨林、次生林和专类园,聚焦于环境指示物种蝴蝶这一类群,通过样线法系统调查一年内蝴蝶多样性及其变化。观测结果显示：蝴蝶在版纳植物园内全年发生,共调查到其成虫5科126属218种6 015头,其中蛱蝶科多样性最高。蝴蝶种类及数量随月动态变化,生境间有差异,7-8月种类和数量达到最高峰;1月种类最少,而5-6月数量最低;每月均出现的种类仅有12种,绝大部分种类分散发生于不同月份。影响蝴蝶群落多样性的气候因子中,月最高温显著影响蝴蝶群落的物种丰富度和数量,月最低温显著影响物种丰富度、香农多样性和辛普森多样性,月平均温仅显著影响香农多样性。在版纳的三个典型季节中蝴蝶多样性存在差异,雨季物种丰富度最高,干热季香农和辛普森指数最高;雨季和雾凉季蝴蝶群落组成差异大,仅雾凉季与干热季的蝴蝶群落呈现中等程度相似。此外,在片段化雨林、次生林和专类园这3种不同生境中,蝴蝶群落组成也存在差异,蝴蝶物种丰富度和香农指数在次生林中最高,而辛普森指数则是片段化雨林最高;仅次生林与片段化雨林的蝴蝶群落呈现出中等程度相似。本研究揭示了版纳植物园蝴蝶群落的种类组成与月动态变化规律,并明确了不同季节和生境中蝴蝶群落的多样性变化,可为区域蝴蝶多样性观测及保护提供参考依据。     

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

Large populations of bacteria live on leaf surfaces and these phyllosphere bacteria can have important effects on plant health. However, we currently have a limited understanding of bacterial diversity on tree leaves and the inter‐ and intra‐specific variability in phyllosphere community structure. We used a barcoded pyrosequencing technique to characterize the bacterial communities from leaves of 56 tree species in Boulder, Colorado, USA, quantifying the intra‐ and inter‐individual variability in the bacterial communities from 10 of these species. We also examined the geographic variability in phyllosphere communities on Pinus ponderosa from several locations across the globe. Individual tree species harboured high levels of bacterial diversity and there was considerable variability in community composition between trees. The bacterial communities were organized in patterns predictable from the relatedness of the trees as there was significant correspondence between tree phylogeny and bacterial community phylogeny. Inter‐specific variability in bacterial community composition exceeded intra‐specific variability, a pattern that held even across continents where we observed minimal geographic differentiation in the bacterial communities on P. ponderosa needles.     

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola

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 changes in land use in the tropics on species and trait composition of Collembola communities is very limited. We investigated the response of Collembola to the conversion of rainforest into rubber agroforestry (“jungle rubber”), rubber, and oil palm plantations in Jambi Province (Sumatra, Indonesia), a region which experienced one of the strongest recent deforestation globally. Collembola were sampled in 2013 and 2016 from the litter and soil layer using heat extraction, and environmental factors were measured (litter C/N ratio, pH, water content, composition of microbial community and predator abundance). In the litter layer, density and species richness in plantation systems were 25%–38% and 30%–40% lower, respectively, than in rainforest. However, in the soil layer, density, species richness, and trait diversity of Collembola were only slightly affected by land‐use change, contrasting the response of many other animal groups. Species and trait composition of Collembola communities in litter and soil differed between each of the land‐use systems. Water content and pH were identified as main factors related to the differences in species and trait composition in both litter and soil, followed by the density of micro‐ and macropredators. Dominant species of Collembola in rainforest and jungle rubber were characterized by small body size, absence of furca, and absence of intense pigmentation, while in plantations, larger species with long furca and diffuse or patterned pigmentation were more abundant. Overall, land‐use change negatively affected Collembola communities in the litter layer, but its impact was lower in the soil layer. Several pantropical genera of Collembola (i.e., Isotomiella, Pseudosinella, and Folsomides) dominated across land‐use systems, reflecting their high environmental adaptability and/or efficient dispersal, calling for studies on their ecology and genetic diversity. The decline in species richness and density of litter‐dwelling Collembola with the conversion of rainforest into plantation systems calls for management practices mitigating negative effects of the deterioration of the litter layer in rubber plantations, but even more in oil palm plantations.