Logged peat swamp forest supports greater macrofungal biodiversity than large‐scale oil palm plantations and smallholdings

Intensive land expansion of commercial oil palm agricultural lands results in reducing the size of peat swamp forests, particularly in Southeast Asia. The effect of this land conversion on macrofungal biodiversity is, however, understudied. We quantified macrofungal biodiversity by identifying mushroom sporocarps throughout four different habitats; logged peat swamp forest, large‐scale oil palm plantation, monoculture, and polyculture smallholdings. We recorded a total of 757 clusters of macrofungi belonging to 127 morphospecies and found that substrates for growing macrofungi were abundant in peat swamp forest; hence, morphospecies richness and macrofungal clusters were significantly greater in logged peat swamp forest than converted oil palm agriculture lands. Environmental factors that influence macrofungi in logged peat swamp forests such as air temperature, humidity, wind speed, soil pH, and soil moisture were different from those in oil palm plantations and smallholdings. We conclude that peat swamp forests are irreplaceable with respect to macrofungal biodiversity. They host much greater macrofungal biodiversity than any of the oil palm agricultural lands. It is imperative that further expansion of oil palm plantation into remaining peat swamp forests should be prohibited in palm oil producing countries. These results imply that macrofungal distribution reflects changes in microclimate between habitats and reduced macrofungal biodiversity may adversely affect decomposition in human‐modified landscapes.     

Replanting of first‐cycle oil palm results in a second wave of biodiversity loss

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Keep wetlands wet: the myth of sustainable development of tropical peatlands – implications for policies and management

Pristine tropical peat swamp forests (PSFs) represent a unique wetland ecosystem of distinctive hydrology which support unique biodiversity and globally significant stores of soil carbon. Yet in Indonesia and Malaysia, home to 56% of the world's tropical peatland, they are subject to considerable developmental pressures, including widespread drainage to support agricultural needs. In this article, we review the ecology behind the functioning and ecosystem services provided by PSFs, with a particular focus on hydrological processes as well as the role of the forest itself in maintaining those services. Drawing on this, we review the suitability of current policy frameworks and consider the efficacy of their implementation. We suggest that policies in Malaysia and Indonesia are often based around the narrative of oil palm and other major monocrops as drivers of prosperity and development. However, we also argue that this narrative is also being supported by a priori claims concerning the possibility of sustainability of peat swamp exploitation via drainage‐based agriculture through the adherence to best management practices. We discuss how this limits their efficacy, uptake and the political will towards enforcement. Further, we consider how both narratives (prosperity and sustainability) clearly exclude important considerations concerning the ecosystem value of tropical PSFs which are dependent on their unimpacted hydrology. Current research clearly shows that the actual debate should be focused not on how to develop drainage‐based plantations sustainably, but on whether the sustainable conversion to drainage‐based systems is possible at all.     

Impacts of logging and conversion of rainforest to oil palm on the functional diversity of birds in Sundaland

Commercial selective logging and the conversion of primary and degraded forests to agriculture are the biggest threats to tropical biodiversity. Our understanding of the impacts of these disturbances and the resulting local extinctions on the functional roles performed by the remaining species is limited. We address this issue by examining functional diversity (FD), which quantifies a range of traits that affect a species' ecological role in a community as a single continuous metric. We calculated FD for birds across a gradient of disturbance from primary forest through intensively logged forest to oil palm plantations on previously forested land in Borneo, Southeast Asia, a hotspot of imperilled biodiversity. Logged rainforest retained similar levels of FD to unlogged rainforest, even after two logging rotations, but the conversion of logged forest to oil palm resulted in dramatic reductions in FD. The few remaining species in oil palm filled a disproportionately wide range of functional roles but showed very little clustering in terms of functional traits, suggesting that any further extinctions from oil palm would reduce FD even further. Determining the extent to which the changes we recorded were due to under‐utilization of resources within oil palm or a reduction in the resources present is an important next step. Nonetheless our study improves our understanding of the stability and resilience of functional diversity in these ecosystems and of the implications of land‐use changes for ecosystem functioning.     

Minimizing the biodiversity impact of Neotropical oil palm development

Oil palm agriculture is rapidly expanding in the Neotropics, at the expense of a range of natural and seminatural habitats. A key question is how this expansion should be managed to reduce negative impacts on biodiversity. Focusing on the Llanos of Colombia, a mixed grassland–forest system identified as a priority zone for future oil palm development, we survey communities of ants, dung beetles, birds and herpetofauna occurring in oil palm plantations and the other principal form of agriculture in the region – improved cattle pasture – together with those of surrounding natural forests. We show that oil palm plantations have similar or higher species richness across all four taxonomic groups than improved pasture. For dung beetles, species richness in oil palm was equal to that of forest, whereas the other three taxa had highest species richness in forests. Hierarchical modelling of species occupancy probabilities indicated that oil palm plantations supported a higher proportion of species characteristic of forests than did cattle pastures. Across the bird community, occupancy probabilities within oil palm were positively influenced by increasing forest cover in a surrounding 250 m radius, whereas surrounding forest cover did not strongly influence the occurrence of other taxonomic groups in oil palm. Overall, our results suggest that the conversion of existing improved pastures to oil palm has limited negative impacts on biodiversity. As such, existing cattle pastures of the Colombian Llanos could offer a key opportunity to meet governmental targets for oil palm development without incurring significant biodiversity costs. Our results also highlight the value of preserving remnant forests within these agricultural landscapes, protecting high biodiversity and exporting avian ‘spill‐over’ effects into oil palm plantations.     

Do riparian reserves support dung beetle biodiversity and ecosystem services in oil palm-dominated tropical landscapes?

Agricultural expansion and intensification are major threats to global biodiversity, ecological functions, and ecosystem services. The rapid expansion of oil palm in forested tropical landscapes is of particular concern given their high biodiversity. Identifying management approaches that maintain native species and associated ecological processes within oil palm plantations is therefore a priority. Riparian reserves are strips of forest retained alongside rivers in cultivated areas, primarily for their positive hydrological impact. However, they can also support a range of forest‐dependent species or ecosystem services. We surveyed communities of dung beetles and measured dung removal activity in an oil palm‐dominated landscape in Sabah, Malaysian Borneo. The species richness, diversity, and functional group richness of dung beetles in riparian reserves were significantly higher than in oil palm, but lower than in adjacent logged forests. The community composition of the riparian reserves was more similar to logged forest than oil palm. Despite the pronounced differences in biodiversity, we did not find significant differences in dung removal rates among land uses. We also found no evidence that riparian reserves enhance dung removal rates within surrounding oil palm. These results contrast previous studies showing positive relationships between dung beetle species richness and dung removal in tropical forests. We found weak but significant positive relationships between riparian reserve width and dung beetle diversity, and between reserve vegetation complexity and dung beetle abundance, suggesting that these features may increase the conservation value of riparian reserves. Synthesis and applications: The similarity between riparian reserves and logged forest demonstrates that retaining riparian reserves increases biodiversity within oil palm landscapes. However, the lack of correlation between dung beetle community characteristics and dung removal highlights the need for further research into spatial variation in biodiversity–ecosystem function relationships and how the results of such studies are affected by methodological choices.     

Spiders in canopy and ground microhabitats are robust to changes in understory vegetation management practices in mature oil palm plantations (Riau,Indonesia)

Conversion of natural habitats to oil palm agriculture has caused declines in biodiversity and changes in ecosystem functions. To preserve biodiversity we must protect natural habitats, but once oil palm plantations are established, developing more-environmentally friendly management strategies could support higher levels of within-plantation biodiversity and boost the delivery of ecosystem services, possibly increasing oil palm productivity. In this study, we use a before-after control-impact (BACI) experiment to test whether three understory vegetation management strategies affect spider abundance, species richness, and species-level community composition in canopy and ground microhabitats in mature oil palm plantations. Our treatments encompassed the range of current management practices and included heavy applications of herbicides to eliminate all understory vegetation, maintaining some understory vegetation using business-as-usual herbicide applications, and enhancing understory vegetation by not applying any herbicides. We focussed on spiders, as they are both biologically and economically important in oil palm plantations, owing to their important pest control services. We identified more than 1000 spiders, representing 20 families and 83 morphospecies. The treatments did not affect any aspects of spider biodiversity, although the abundance and species richness of canopy-dwelling spiders changed between pre- and post-treatment sample periods, independent of treatment. Our findings indicate that differences in understory vegetation management practices do not affect spiders, or the pest management services that they provide, in mature oil palm plantations. As such, more extreme changes in management would probably be required to enhance spider biodiversity in oil palm plantations in the long-term. Further studies are needed to determine the practicalities of such approaches, to assess how changes in vegetation management practices affect spiders in additional microhabitats, and how the impacts of such approaches vary across the 20–30 year oil palm commercial life cycle.     

Reconciling Oil Palm Expansion and Climate Change Mitigation in Kalimantan,Indonesia

Our society faces the pressing challenge of increasing agricultural production while minimizing negative consequences on ecosystems and the global climate. Indonesia, which has pledged to reduce greenhouse gas (GHG) emissions from deforestation while doubling production of several major agricultural commodities, exemplifies this challenge. Here we focus on palm oil, the world’s most abundant vegetable oil and a commodity that has contributed significantly to Indonesia’s economy. Most oil palm expansion in the country has occurred at the expense of forests, resulting in significant GHG emissions. We examine the extent to which land management policies can resolve the apparently conflicting goals of oil palm expansion and GHG mitigation in Kalimantan, a major oil palm growing region of Indonesia. Using a logistic regression model to predict the locations of new oil palm between 2010 and 2020 we evaluate the impacts of six alternative policy scenarios on future emissions. We estimate net emissions of 128.4–211.4 MtCO₂ yr^-1 under business as usual expansion of oil palm plantations. The impact of diverting new plantations to low carbon stock land depends on the design of the policy. We estimate that emissions can be reduced by 9-10% by extending the current moratorium on new concessions in primary forests and peat lands, 35% by limiting expansion on all peat and forestlands, 46% by limiting expansion to areas with moderate carbon stocks, and 55–60% by limiting expansion to areas with low carbon stocks. Our results suggest that these policies would reduce oil palm profits only moderately but would vary greatly in terms of cost-effectiveness of emissions reductions. We conclude that a carefully designed and implemented oil palm expansion plan can contribute significantly towards Indonesia’s national emissions mitigation goal, while allowing oil palm area to double.     

Predation of potential insect pests in oil palm plantations,rubber tree plantations,and fruit orchards

In human‐modified landscapes, important ecological functions such as predation are negatively affected by anthropogenic activities, including the use of pesticides and habitat degradation. Predation of insect pests is an indicator of healthy ecosystem functioning, which provides important ecosystem services, especially for agricultural systems. In this study, we compare predation attempts from arthropods, mammals, and birds on artificial caterpillars in the understory, between three tropical agricultural land‐use types: oil palm plantations, rubber tree plantations, and fruit orchards. We collected a range of local and landscape‐scale data including undergrowth vegetation structure; elevation; proximity to forest; and canopy cover in order to understand how environmental variables can affect predation. In all three land‐use types, our results showed that arthropods and mammals were important predators of artificial caterpillars and there was little predation by birds. We did not find any effect of the environmental variables on predation. There was an interactive effect between land‐use type and predator type. Predation by mammals was considerably higher in fruit orchards and rubber tree than in oil palm plantations, likely due to their ability to support higher abundances of insectivorous mammals. In order to maintain or enhance natural pest control in these common tropical agricultural land‐use types, management practices that benefit insectivorous animals should be introduced, such as the reduction of pesticides, improvement of understory vegetation, and local and landscape heterogeneity.     

Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.     

How will oil palm expansion affect biodiversity?

Oil palm is one of the world's most rapidly increasing crops. We assess its contribution to tropical deforestation and review its biodiversity value. Oil palm has replaced large areas of forest in Southeast Asia, but land-cover change statistics alone do not allow an assessment of where it has driven forest clearance and where it has simply followed it. Oil palm plantations support much fewer species than do forests and often also fewer than other tree crops. Further negative impacts include habitat fragmentation and pollution, including greenhouse gas emissions. With rising demand for vegetable oils and biofuels, and strong overlap between areas suitable for oil palm and those of most importance for biodiversity, substantial biodiversity losses will only be averted if future oil palm expansion is managed to avoid deforestation.     

Sensitivity and resistance of soil fertility indicators to land-use changes: New concept and examples from conversion of Indonesian rainforest to plantations

Tropical forest conversion to agricultural land leads to a strong decrease of soil organic carbon (SOC) stocks. While the decrease of the soil C sequestration function is easy to measure, the impacts of SOC losses on soil fertility remain unclear. Especially the assessment of the sensitivity of other fertility indicators as related to ecosystem services suffers from a lack of clear methodology. We developed a new approach to assess the sensitivity of soil fertility indicators and tested it on biological and chemical soil properties affected by rainforest conversion to plantations. The approach is based on (non-)linear regressions between SOC losses and fertility indicators normalized to their level in a natural ecosystem. Biotic indicators (basal respiration, microbial biomass, acid phosphatase), labile SOC pools (dissolved organic carbon and light fraction) and nutrients (total N and available P) were measured in Ah horizons from rainforests, jungle rubber, rubber (Hevea brasiliensis) and oil palm (Elaeis guineensis) plantations located on Sumatra. The negative impact of land-use changes on all measured indicators increased in the following sequence: forest < jungle rubber < rubber < oil palm. The basal respiration, microbial biomass and nutrients were resistant to SOC losses, whereas the light fraction was lost stronger than SOC. Microbial C use efficiency was independent on land use. The resistance of C availability for microorganisms to SOC losses suggests that a decrease of SOC quality was partly compensated by litter input and a relative enrichment by nutrients. However, the relationship between the basal respiration and SOC was non-linear; i.e. negative impact on microbial activity strongly increased with SOC losses. Therefore, a small decrease of C content under oil palm compared to rubber plantations yielded a strong drop in microbial activity. Consequently, management practices mitigating SOC losses in oil palm plantations would strongly increase soil fertility and ecosystem stability. We conclude that the new approach enables quantitatively assessing the sensitivity and resistance of diverse soil functions to land-use changes and can thus be used to assess resilience of agroecosystems with various use intensities.     

Effects of Logging and Oil Palm Expansion on Stream Frog Communities on Borneo,Southeast Asia

The conversion of tropical rain forests to oil palm plantations is a major threat to Southeast Asia's rich biodiversity. Fostering forest species communities in secondary forests, agroforestry systems, and plantations is therefore increasingly becoming a conservation focus. This study uses standardized transect‐based sampling to compare species richness, density and community composition of stream anuran assemblages among primary forests, repeatedly logged forests and oil palm plantations in northern Borneo. In primary forest streams, we recorded an average of 19 frog species, compared to 15 species in logged forests and 11 species in oil palm plantation streams. However, the high percentage of canopy cover above the plantation streams mitigated this loss to some extent. This study corroborates numerous studies that oil palm plantations have mainly negative effects on the region's biodiversity. However, our results also demonstrate the high conservation value of logged forests for Bornean stream‐dependent anurans. We conclude that palm plantations have a largely unused potential to promote regional anuran biodiversity.     

Establishing the evidence base for maintaining biodiversity and ecosystem function in the oil palm landscapes of South East Asia

The conversion of natural forest to oil palm plantation is a major current threat to the conservation of biodiversity in South East Asia. Most animal taxa decrease in both species richness and abundance on conversion of forest to oil palm, and there is usually a severe loss of forest species. The extent of loss varies significantly across both different taxa and different microhabitats within the oil palm habitat. The principal driver of this loss in diversity is probably the biological and physical simplification of the habitat, but there is little direct evidence for this. The conservation of forest species requires the preservation of large reserves of intact forest, but we must not lose sight of the importance of conserving biodiversity and ecosystem processes within the oil palm habitat itself. We urgently need to carry out research that will establish whether maintaining diversity supports economically and ecologically important processes. There is some evidence that both landscape and local complexity can have positive impacts on biodiversity in the oil palm habitat. By intelligent manipulation of habitat complexity, it could be possible to enhance not only the number of species that can live in oil palm plantations but also their contribution to the healthy functioning of this exceptionally important and widespread landscape.     

Degradation of Root Community Traits as Indicator for Transformation of Tropical Lowland Rain Forests into Oil Palm and Rubber Plantations

Conversion of tropical forests into intensely managed plantations is a threat to ecosystem functions. On Sumatra, Indonesia, oil palm (Elaeis guineensis) plantations are rapidly expanding, displacing rain forests and extensively used rubber (Hevea brasiliensis) agro-forests. Here, we tested the influence of land use systems on root traits including chemical traits (carbon, nitrogen, mineral nutrients, potentially toxic elements [aluminium, iron] and performance traits (root mass, vitality, mycorrhizal colonization). Traits were measured as root community-weighed traits (RCWTs) in lowland rain forests, in rubber agro-forests mixed with rain forest trees, in rubber and oil palm plantations in two landscapes (Bukit Duabelas and Harapan, Sumatra). We hypothesized that RCWTs vary with land use system indicating increasing transformation intensity and loss of ecosystem functions. The main factors found to be related to increasing transformation intensity were declining root vitality and root sulfur, nitrogen, carbon, manganese concentrations and increasing root aluminium and iron concentrations as well as increasing spore densities of arbuscular mycorrhizas. Mycorrhizal abundance was high for arbuscular and low for ectomycorrhizas and unrelated to changes in RCWTs. The decline in RCWTs showed significant correlations with soil nitrogen, soil pH and litter carbon. Thus, our study uncovered a relationship between deteriorating root community traits and loss of ecosystem functionality and showed that increasing transformation intensity resulted in decreasing root nutrition and health. Based on these results we suggest that land management that improves root vitality may enhance the ecological functions of intense tropical production systems.     

Poor Prospects for Avian Biodiversity in Amazonian Oil Palm

Expansion of oil palm plantations across the humid tropics has precipitated massive loss of tropical forest habitats and their associated speciose biotas. Oil palm plantation monocultures have been identified as an emerging threat to Amazonian biodiversity, but there are no quantitative studies exploring the impact of these plantations on the biome’s biota. Understanding these impacts is extremely important given the rapid projected expansion of oil palm cultivation in the basin. Here we investigate the biodiversity value of oil palm plantations in comparison with other dominant regional land-uses in Eastern Amazonia. We carried out bird surveys in oil palm plantations of varying ages, primary and secondary forests, and cattle pastures. We found that oil palm plantations retained impoverished avian communities with a similar species composition to pastures and agrarian land-uses and did not offer habitat for most forest-associated species, including restricted range species and species of conservation concern. On the other hand, the forests that the oil palm companies are legally obliged to protect hosted a relatively species-rich community including several globally-threatened bird species. We consider oil palm to be no less detrimental to regional biodiversity than other agricultural land-uses and that political pressure exerted by large landowners to allow oil palm to count as a substitute for native forest vegetation in private landholdings with forest restoration deficits would have dire consequences for regional biodiversity.     

Neotropical moth assemblages degrade due to oil palm expansion

Oil palm is one of the most rapidly expanding crops throughout the tropics, yet little is known about its impacts on Neotropical invertebrate biodiversity. Responses of insect assemblages to land conversion may substantially vary among taxa. We assessed geometrid and arctiine moth assemblages in a Costa Rican human dominated landscape, where oil palm plantations are now the second most common land cover. Moths were sampled during 6 months with automatic traps in the interior and margin of old-growth forests, young secondary forests and oil palm plantations in a 30 km² area. Our results show that richness and diversity of both taxa were severely reduced in oil palm compared to all other habitats. Geometrid abundance was highest in forest interiors and lowest in oil palm, while arctiine numbers did not differ between habitats. Dominance was highest in oil palm plantations, where one arctiine species and one geometrid species accounted for over 40% of total abundance in each of their respective taxa. Species composition was distinct in oil palm and forest interior sites, and depicted a gradient of habitat disturbance in ordination space that was strongly related to vegetation diversity and structure. This study demonstrates that oil palm plantations are not a suitable habitat for these moth taxa. Whilst some arctiine species seem adapted to disturbed habitats, geometrids were more dependent on old-growth forests, showing higher bioindicator potential. In the face of accelerated oil palm expansion, conservation strategies should focus on protecting old-growth forest remnants, as well as increasing species diversity and structural complexity of degraded habitats.     

Land Use Changes and GHG Emissions from Tropical Forest Conversion by Oil Palm Plantations in Riau Province,Indonesia

Increasing prices and demand for biofuel and cooking oil from importer countries have caused a remarkable expansion of oil palm plantations in Indonesia. In this paper, we attempt to monitor the expansion of oil palm plantations on peat land and in tropical forests. We measure the GHG emissions from the land conversion activities at provincial scale. Using Landsat images from three different periods (1990s, 2000s and 2012), we classified LULC of the Riau Province, which is the largest oil palm producing region in Indonesia. A hybrid method of integration, generated by combining automatic processing and manual analysis, yields the best results. We found that the tropical rainforest cover decreased from ∼63% in the 1990s to ∼37% in the 2000s. By 2012, the remaining tropical rainforest cover was only ∼22%. From the 1990s to the 2000s, conversion of forests and peat lands was the primary source of emissions, total CO₂ emitted to the atmosphere was estimated at ∼26.6 million tCO₂.y^-1, with 40.62% and 59.38% of the emissions from conversion of peat lands and forests, respectively. Between 2000 and 2012, the total CO₂ emitted to the atmosphere was estimated at ∼5.2 million tCO₂. y^-1, with 69.94% and 27.62% of the emissions from converted peat lands and converted forests, respectively. The results show that in the Riau Province, the oil palm industry boomed in the period from 1990 to 2000, with transformation of tropical forest and peat land as the primary source of emissions. The decrease of CO₂ emissions in the period from 2000 to 2012 is possibly due to the enforcement of a moratorium on deforestation.     

Impacts of oil palm plantations on changes in environmental heterogeneity and Heteroptera (Gerromorpha and Nepomorpha) diversity

This study evaluates the effects of oil palm plantations on environmental heterogeneity and diversity (α and β) of aquatic Heteroptera (semi-aquatic and aquatic species) in Amazon streams. We assessed eight streams located in forested areas and 12 in oil palm plantations. As expected, oil palm areas had lower environmental heterogeneity, despite the presence of riparian vegetation. Heteropteran communities differed in forest and oil palm areas, however, only semi-aquatic bugs were affected by environmental variables. Streams in oil palm plantations had lower α-diversity and distinct community structures when compared to forest sites. Oil palm plantation did not affect the β-diversity of semi-aquatic bugs, however, there was increased β-diversity of aquatic bugs in these areas. These results reflect the impacts of environmental heterogeneity generated by plantations next to riparian vegetation, inducing local diversity loss. Effects on β-diversity differed among groups of Heteroptera, mainly due to the differences in the life histories of each group. Semi-aquatic bugs seem to undergo environmental filtering, while aquatic bugs can be structured by limiting similarity. Thus, the management and land conservation strategies adopted to preserve ecosystems within oil palm plantations were insufficient for the protection of aquatic heteropteran communities. In summary, such conservation policies should account for the particularities of different groups of the aquatic ecosystem; especially for aquatic fauna, which are usually overlooked in conservation policies for the Brazilian Amazon.     

The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land‐use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once‐logged and twice‐logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell–cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land‐use changes on the interaction of soil microbes.