Soil nitrogen dynamics as an indicator for longleaf pine restoration

Assessing the status of soil nutrients with their corresponding microbial communities provides important information about degraded soils during the restoration of coastal wet pine forests. Net nitrogen mineralization, nitrogen‐oxidizing bacteria (NOB), and soil microbial biomass were compared with patch‐derived volume along a 110‐year longleaf pine (Pinus palustris Mill.) chronosequence for identifying a trajectory and ecological benchmark during forest restoration. Net nitrogen mineralization rates decreased significantly in the maturing‐aged, pine patches, driven by a larger drop in net nitrification. Net nitrification and abundance of NOB were higher in young pine patches compared to soils from the maturing (86–110 years) pine patches. Gross nitrate fluxes followed the nonfungal portion of the soil microbial biomass along the chronosequence, declining in 64‐year‐old pine patches. Microbial biomass peaked in patches 17–34 years of age, but significantly declined in the older patches. Fungal biomass leveled off without decline. Ammonium was the major source of nitrogen within the maturing pine patches as well as the wetland patches, indicating that ammonium maintains longleaf pine during growth‐limiting conditions. Nitrate dominated during rapid tree growth, optimally in mesic conditions. The relative amounts of available ammonium to nitrate can be used to model nitrogen cycling in facultative‐wetland pine forests of the coastal United States as soils alternate between wet and mesic conditions. A key restoration benchmark occurred after 86 years of pine development when pine patch growth rates slowed, with lower numbers of NOB, when the nonfungal biomass leveled off, and net nitrification rates are at a minimum, during pine maturation.     

A bioprocess for the remediation of anaerobically digested molasses spentwash from biogas plant and simultaneous production of lactic acid

A bacterial isolate LAB-1 identified as Lactobacillus casei was cultivated in a fermentation medium containing biogas plant effluent. This effluent was generated after anaerobic digestion of molasses spentwash in biogas fermenters. In the bioremediation process of this very dark coloured effluent through the cultivation of L. casei, decrease in effluent's colour of 49 and 52% and reduction in COD level up to 54 and 57% were achieved using bacterial cells in free and immobilised system, respectively, in 5 days batch cultivation. During this process of bioremediation, a metabolite lactic acid was produced by this bacterial isolate with the yield of 10.9 and 11.3 mg/ml, in free and immobilised cells fermentation, respectively.     

Interspecific competition enhances nitrogen fixation in an actinorhizal shrub

In forest understory restoration, the establishment of reintroduced species may be strongly linked to their ability to compete for belowground resources. In this study, we provide isotopic and morphological evidence for competition-induced increases in nitrogen fixation by Morella cerifera (L.) Small (wax myrtle) when planted with Pinus palustris Mill (longleaf pine). Compared to a competition-free treatment, we found no significant differences in tissue N concentrations for M. cerifera. However, ¹⁵N enrichment in leaves, stems and roots, as well as whole-plant values for nitrogen derived from fertilizer were significantly lower when the plants were subject to interspecific competition from P. palustris. Plants in the competition treatment also allocated a significantly greater percentage of belowground biomass to root nodules than those in the competition-free treatment (0.65 vs. 0.41%). This strongly suggests that M. cerifera is capable of upregulating nitrogen fixation in response to interspecific competition. This may help explain why M. cerifera outperformed non-nitrogen-fixing species reintroduced on the same site.     

CRL3IBTK Regulates the Tumor Suppressor Pdcd4 through Ubiquitylation Coupled to Proteasomal Degradation

The human inhibitor of Bruton''s tyrosine kinase isoform α (IBtkα) is a BTB protein encoded by the IBTK gene, which maps to chromosomal locus 6q14.1, a mutational hot spot in lymphoproliferative disorders. Here, we demonstrate that IBtkα forms a CRL3^IBTK complex promoting its self-ubiquitylation. We identified the tumor suppressor Pdcd4 as IBtkα interactor and ubiquitylation substrate of CRL3^IBTK for proteasomal degradation. Serum-induced degradation of Pdcd4 required both IBtkα and Cul3, indicating that CRL3^IBTK regulated the Pdcd4 stability in serum signaling. By promoting Pdcd4 degradation, IBtkα counteracted the suppressive effect of Pdcd4 on translation of reporter luciferase mRNAs with stem-loop structured or unstructured 5′-UTR. IBtkα depletion by RNAi caused Pdcd4 accumulation and decreased the translation of Bcl-xL mRNA, a well known target of Pdcd4 repression. By characterizing CRL3^IBTK as a novel ubiquitin ligase, this study provides new insights into regulatory mechanisms of cellular pathways, such as the Pdcd4-dependent translation of mRNAs.     

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

Background

In humans it is unknown if the composition of the gut microbiota alters the risk of Plasmodium falciparum infection or the risk of developing febrile malaria once P. falciparum infection is established. Here we collected stool samples from a cohort composed of 195 Malian children and adults just prior to an intense P. falciparum transmission season. We assayed these samples using massively parallel sequencing of the 16S ribosomal RNA gene to identify the composition of the gut bacterial communities in these individuals. During the ensuing 6-month P. falciparum transmission season we examined the relationship between the stool microbiota composition of individuals in this cohort and their prospective risk of both P. falciparum infection and febrile malaria.

Results

Consistent with prior studies, stool microbial diversity in the present cohort increased with age, although the overall microbiota profile was distinct from cohorts in other regions of Africa, Asia and North America. Age-adjusted Cox regression analysis revealed a significant association between microbiota composition and the prospective risk of P. falciparum infection; however, no relationship was observed between microbiota composition and the risk of developing febrile malaria once P. falciparum infection was established.

Conclusions

These findings underscore the diversity of gut microbiota across geographic regions, and suggest that strategic modulation of gut microbiota composition could decrease the risk of P. falciparum infection in malaria-endemic areas, potentially as an adjunct to partially effective malaria vaccines.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1819-3) contains supplementary material, which is available to authorized users.     

Evolution of allostery in the cyclic nucleotide binding module

Background  

The cyclic nucleotide binding (CNB) domain regulates signaling pathways in both eukaryotes and prokaryotes. In this study, we analyze the evolutionary information embedded in genomic sequences to explore the diversity of signaling through the CNB domain and also how the CNB domain elicits a cellular response upon binding to cAMP.