Selective logging

Selective logging is the logging practice of entering a forest and only removing some trees, usually those which are unhealthy or in dense areas. Sometimes the logging is performed on the ground, but to not harm surrounding forest, it is more often done by air using a helicopter. Selective logging has been well-documented to improve forest health and reduce the dangers of wildfire and has been endorsed by the National Forest Service as the better alternative to clear-cutting. It is also supported by the UN. Another advantage is that through selection of which trees to log, rare species can be saved from the logger's saw. (Conservapedia)

It is true, selective logging doesn't have a strong impact on the overall species richness and diversity of tropical forest, however, it has been shown that this can vary considerably depending on the intensity of logging. This could result in changes in the composition of species, as forest-interior specialists disappear and are replaced with edge-tolerant, gap specialists. What's even more important is what happens after logging. The conversion of logged forest to agricultural land uses has a far greater negative impact on biodiversity than logging alone. Conversion to agriculture results in a major reduction in biodiversity. It is affecting a wide range of organisms and because it changes soil pH, carbon and nutrient content, it can cause major shifts in soil microbial communities such as fungi. These play crucial roles in the ecosystem as decomposers, pathogens and plant symbionts. Despite this, little has has been done in the tropics to assess the effect of land use changes on soil fungal communities.

Palm oil cultivation has been heavily criticized for severe environmental impacts especially through increased deforestation. Aside from its use as a food ingredient  it is increasingly used to produce biodiesel. However, the deforestation caused by oil palm plantations is perhaps more damaging to the climate than the benefits gained by switching to biofuel and that doesn't even includes the effects on the local biodiversity.

A new soil fungal community study looked at the effects caused by different intensities of logging. Researchers tried to evaluate if conversion of forest to oil palm plantation has a stronger impact on soil fungi than logging, as is the case for many other taxa. They utilized next generation technology to obtain fungal DNA Barcodes (ITS1 region) from extracted soil DNA. The results were used to compare communities of soil fungi between unlogged, once-logged, and twice-logged rainforest, as well as areas cleared for oil palm, in Sabah, Malaysia. 

Overall fungal community composition differed significantly between forest and oil palm plantation. The OTU richness and Chao 1 were higher in forest, compared to oil palm plantation. As a proportion of total reads, Basidiomycota were more abundant in forest soil, compared to oil palm plantation soil. The turnover of fungal OTUs across space, true β-diversity, was also higher in forest than oil palm plantation. Ectomycorrhizal (EcM) fungal abundance was significantly different between land uses, with highest relative abundance (out of total fungal reads) observed in unlogged forest soil, lower abundance in logged forest, and lowest in oil palm. In their entirety, these results indicate a pervasive effect of conversion to oil palm on fungal community structure.

Even from a more economic point of view this is alarming because radical changes in fungal communities might impact the long-term sustainability of oil palm agriculture. The results also show that logging has more subtle long term effects on the relative abundance of ectomycorrhizal fungi, which might affect tree recruitment and nutrient cycling . They are the fungal partner of the symbiosis between fungi and the roots of various plant especially tree species. However, to my surprise, in general the logged forest retains most of the diversity and community composition of unlogged forest. 

So, logged forest might not be an irretrievably damaged and violently altered system. Actually, protecting it from conversion to oil palm plantation may have considerable conservation benefits.