The present study determined the abundance of genes/molecules, subsystems and taxa of microbes involved in wood decomposition and soil in an attempt to provide a wider view of the possible interactions. The distinctiveness of the subsystems in the decaying log (when compared to soil), clearly supports the uniqueness of the microbial communities in this setting. Moreover, the separate clustering of the EY log and composite sample supports the uniqueness of the decaying wood as well. Composite was chosen as a reference sample microbial processes in this type of sample could be very similar to those taking place in decaying wood (Miyatake and Iwabuchi, 2006). Although this was not the case, it is possible that the microbial communities at another step of composite decomposition may be similar to the microbial processes in decaying wood. Notably, calculated diversity indexes suggest that microbial diversity is generally higher in the tropics. However, this point is still unresolved; latitude may place an upper limit on microbial diversity but is not believed to be the primary determinant. QS subsystems of tropical soils exhibited a similarity of 80% with the Waseca soil. This suggests that certain QS subsystems may be conserved while individual species may differ, and is analogous to the conservation of homologous protein structures, while the respective amino acid sequences may vary considerably.
Wood is structurally complex, and its decomposition involves a succession of different groups of organisms. Degradation of components of wood by one organism provides substrates for other organisms (for example, cleavage of lignocellulose by white rot fungi liberates sugars and makes other components accessible), so it can be viewed as a collaborative process. Furthermore, there is spatial delimitation of territory by competing organisms, often intraspecific, and is easily observed as melanized lines of interaction in decaying wood. Parasitism of one guild of wood-decay organisms by others is also common. Given this combination of succession, collaboration, competition and parasitism, it is not surprising that we found evidence of extensive microbial crosstalk in decaying wood.
These types of ecological interaction will depend on the net costs and benefits from the association and will change continuously. For instance, certain intestinal microbes produce metabolites for the benefit of other microbes in mutualistic interaction. It has been suggested that microbes can be “forced” into such interactions by specific mechanisms of QS. This scenario can certainly be applied to decaying wood and soils. Secondary metabolites (as those involved in QS) promote the expression of specific genes involved in processes that occur in wood decomposition and in soil. This genetic expression, which results in specific types of coordinated behaviors, may promote higher abundances of certain microbes. The reason is that the synthesis of molecules that could be beneficial for the proliferation and persistence of specific microbial populations may also be harmful for others (Zhu et al. 1998). Similar outcomes have been reported for activated sludge, in which AHLs mediate the composition and function of the microbial communities. Moreover, microorganisms may also exhibit signal-quenching mechanisms, resistance to antibiotics, toxins and other secondary metabolites, resulting in even more complex interactions. All these processes may have developed in particular microbes that act in specific pathways of wood decomposition and in complex processes in soils.
Mechanisms of microbial communication
The present study is comparable with previous reports of the presence of AHL synthases and LuxR in the Alphaproteobacteria (Koch et al., 2005;Lindum et al., 1998). Even though the bacterial classes were identical in the decaying log and soil, the bacterial species were different. Species related to Phenylobacterium zucineum and Sinorhizobium fredii accounted for AHL synthase genes and luxR in the decaying log, respectively. P. zucineum is an intracellular facultative bacterium recently isolated from the human leukemia cell line K562 (Luo et al., 2008). A similar outcome was noted with S. fredii, which has been characterized as a symbiont of legumes (Krishnan et al., 2003). The presence of these microbes in the log is surprising, but could suggest a possible new role for these bacteria in wood decomposition. The roles of species related to R. sphaeroides or Sulfitobacter spp. in the tropical soil remain to be addressed as well, but these bacteria possess diverse metabolic capabilities and include photosynthesis and nitrogen fixation (as in the case of R. sphaeroides) and chemoorganotrophy (as with Sulfitobacter spp.) (Long et al., 2011;Poole et al., 1989). The particular role of species related to S. fredii in soil represents a matter of further research since these bacteria have been particularly characterized in marine environments. Notably, bacteria harboring AHL synthase genes did not harbor LuxR in the decaying log, and this was not the case for bacteria in the tropical soil. In soil, the same bacterial species accounted for the presence of both AHL synthase genes and luxR. These results suggest that the AHL synthase genes in the decaying log may be luxI homologues. In terms of traR (a homologue of luxR), this gene has been mainly identified in Agrobacterium tumefaciens, which belong to the Alphaproteobacteria. Consistent with previous studies, the highest traR-encoding bacterial abundances in both ecosystems corresponded to the Alphaproteobacteria. Yet, its presence in several bacterial groups was unexpected, suggesting that these sequences may be homologues of traR (Zhu et al., 2011;Swiderska et al., 2001). Bacterial groups harboring genes responsible for the synthesis of AI-2 were more diverse, supporting the universality of this molecule.
Inhibition of microbial communication
More interesting is the greater diversity of bacteria harboring QQ genes. The Alphaproteobacteria (closest match to Citromicrobium bathyomarinum), as reservoirs of AHL acylase genes, were restricted to the decaying log, suggesting a specific role for these microbes in wood decomposition. Similarly, the Gammaproteobacteria accounted for the presence of AHL acylase genes in the decaying log (closest match to Pseudomonas aeruginosa) and soil (species related to Pseudomonas fluorescens and Pseudomonas putida), and similar outcomes were noted with the AHL lactonase genes, which were restricted to the Actinobacteria (species related to Rhodococcus spp.) in both ecosystems. In terms of the AI-2 nucleosidases, the decaying log and soil were characterized by the Alphaproteobacteria and Cytophagia, and the Betaproteobacteria, respectively. This indicates that a greater diversity of bacteria (although different groups) may be involved in quenching the signal produced by bacteria harboring genes responsible for the synthesis of AI-2.
Inhibition of AHL and AI-2 molecules may not represent the only QQ pathways in the ecosystems tested. Results showed that the metabolism of aromatic compounds is well represented in the decaying log and soil. Some aromatic compounds may serve as signaling molecules in microbial communication, as in the case of autoinducer-3, involved in interkingdom signaling; hence, degradation of such signals is feasible (Zhu et al., 1998). Notably, genes involved in the anaerobic degradation of aromatic compounds were more abundant in the decaying log compared to soil, and this is supported by the water-logged nature of the sample.
Little is known about QS in fungi, and certainly less is known about possible QQ signaling pathways. Farnesol has been associated with the overexpression of specific genes, such as cdr1, in fungi of clinical importance (e.g. C. albicans) (Westwater et al., 2005). cdr1 encodes for efflux pumps and its over-expression is considered to be a drug resistance mechanism in C. albicans (Decanis et al. 2011). The presence of cdr1 in species related to Arthroderma gypseum in the decaying log was surprising since this gene has been mainly associated with C. albicans. Cdr1 is a homologue of Mrp1, specific for mammalian cells; therefore, it remains feasible that cdr1 related to A. gypseum represents a homologue of cdr1 present in C. albicans.
Phenazines as mediators of microbial communication
Phenazines are produced by many bacteria that are associated with a host, but less is known about fungi as phenazine-producers (Pierson and Pierson, 2010). In the present study, fungi from the Sordariomycetes accounted for the presence of phenazines in the decaying log and not in the soil. This suggests that the production of phenazines by fungi may be important for wood decomposition and opens the opportunity to characterize their role as phenazine-producers in natural settings. Phenazines were also present in the tropical soil tested and this is consistency with previous reports (Pierson and Pierson, 2010). In humid forests, respiration by microbes and plant roots may limit the availability of oxygen as an electron acceptor. This, in turn, is consistent with the water logged nature of the log from which the dataset was generated.
Resistance mechanisms
Resistance could be the result of the complex microbial interactions in nature. For instance, cobalt-zinc-cadmium resistance was noted in both the decaying log and soil, with greater representation in the soil. This may reflect the higher concentrations of these divalent cations in soil. Results show that ion-resistance in the decaying log and soil is present in various microbial communities, which are not limited to bacteria as fungi have also exhibited resistance to ions (Nies, 1992). Similarly, the presence of genes encoding for multidrug-resistance in pristine environments (as those considered in the present study), supports that antibiotic production is not restricted to clinical settings.
TA systems
TA systems in the decaying wood were more represented than in soil, suggesting that wood decomposition may require the action of a higher diversity of microbes. Several functions have been attributed to the TA systems identified in the decaying log and soil and include: PCD (as in the case of mazEF) (Hazan et al., 2001), persistency and growth control (as with phd/doc) (Magnuson, 2007). PCD in the late stages of wood decomposition and in soil can be the result of the competition for specific nutrients and space and implies a threshold density of related microbes present in the microhabitat. PCD may be induced by antagonistic interactions with competitors.