Long-term chemical and organic fertilization induces distinct variations of microbial associations but unanimous elevation of soil multifunctionality

Intricate microbial associations contribute greatly to the multiple functions (multifunctionality) of natural ecosystems. However, the relationship between microbial associations and soil multifunctionality (SMF) in artificial ecosystems, particularly in agricultural ecosystem with frequent fertilization, remains unclear. In this study, based on a 28-year paddy field experiment, high-throughput sequencing and networks analysis was performed to investigate changes in soil microbial (archaea, bacteria, fungi, and protists) associations and how these changes correlate with SMF under long-term fertilization. Compared to no fertilization (CK), both chemical fertilization with N, P, and K (CF) and chemical fertilization plus rice straw retention (CFR) treatments showed significantly higher soil nutrient content, grain yield, microbial abundance, and SMF. With the exception of archaeal diversity, the CF treatment exhibited the lowest bacterial, fungal, and protist diversity, and the simplest microbial co-occurrence network. In contrast, the CFR treatment had the lowest archaeal diversity, but the highest bacterial, fungal, and protist diversity. Moreover, the CFR treatment exhibited the most complex microbial co-occurrence network with the highest number of nodes, edges, and interkingdom edges. These results highlight that both chemical fertilization with and without straw retention caused high ecosystem multifunctionality while changing microbial association oppositely. Furthermore, these results indicate that rice straw retention contributes to the development of the soil microbiome and ensures the sustainability of high-level ecosystem multifunctionality.

Bipolar Biogeographical Distribution of Parafrancisella Bacteria Carried by the Ciliate Euplotes

Parafrancisella adeliensis, a Francisella-like endosymbiont, was found to reside in the cytoplasm of an Antarctic strain of the bipolar ciliate species, Euplotes petzi. To inquire whether Euplotes cells collected from distant Arctic and peri-Antarctic sites host Parafrancisella bacteria, wild-type strains of the congeneric bipolar species, E. nobilii, were screened for Parafrancisella by in situ hybridization and 16S gene amplification and sequencing. Results indicate that all Euplotes strains analyzed contained endosymbiotic bacteria with 16S nucleotide sequences closely similar to the P. adeliensis 16S gene sequence. This finding suggests that Parafrancisella/Euplotes associations are not endemic to Antarctica, but are common in both the Antarctic and Arctic regions.

Micro-aeration assisted with electrogenic respiration enhanced the microbial catabolism and ammonification of aromatic amines in industrial wastewater

Improvement of refractory nitrogen-containing organics biodegradation is crucial to meet discharged nitrogen standards and guarantee aquatic ecology safety. Although electrostimulation accelerates organic nitrogen pollutants amination, it remains uncertain how to strengthen ammonification of the amination products. This study demonstrated that ammonification was remarkably facilitated under micro-aerobic conditions through the degradation of aniline, an amination product of nitrobenzene, using an electrogenic respiration system. The microbial catabolism and ammonification were significantly enhanced by exposing the bioanode to air. Based on 16S rRNA gene sequencing and GeoChip analysis, our results indicated that aerobic aniline degraders and electroactive bacteria were enriched in suspension and inner electrode biofilm, respectively. The suspension community had a significantly higher relative abundance of catechol dioxygenase genes contributing to aerobic aniline biodegradation and reactive oxygen species (ROS) scavenger genes to protect from oxygen toxicity. The inner biofilm community contained obviously higher cytochrome c genes responsible for extracellular electron transfer. Additionally, network analysis indicated the aniline degraders were positively associated with electroactive bacteria and could be the potential hosts for genes encoding for dioxygenase and cytochrome, respectively. This study provides a feasible strategy to enhance nitrogen-containing organics ammonification and offers new insights into the microbial interaction mechanisms of micro-aeration assisted with electrogenic respiration.

Exploring dynamics and associations of dominant lignocellulose degraders in tomato stalk composting

The plant residues of tomato bring pressures to the environment and composting provides a feasible method to treat such agricultural waste. However, little is known about the succession and associations of the dominant lignocellulose degraders in the compost system. To further accelerate the process by inoculating key functional microorganisms, a compost pile composed of tomato stalk with maize straw addition was constructed, and the whole community structure and functions of the dominant were investigated by applying the integrated mata-omics. Results showed that Actinobacteria, Firmicutes, and Ascomycota dominated and drove the assembly of the co-occurrence network. In the thermophilic stage, Thermobifida was the exclusive degrader of cellulose, and Thermobifida fusca was the most important cellulolytic actinomycete. Saccharomonospora viridis, Planifilum fulgidum, Thermobacillus sp. and the dominant ascomycota of Aspergillus sclerotialis participated in hemicellulose decomposing. In the cooling phase, functional microorganisms became more diverse, with Nocardiopsis flavescens, Glycomyces artemisiae, Glycomyces sambucus, Streptomyces rubrolavendulae and Streptomyces vietnamensis joining the cellulose-degrading rank, and Chaetomium thermophilum emerging as the main hemicellulose degrader. More than two thirds of the bacteria-bacteria interactions and all the fungi-fungi associations were positive, while, both competition (for the same substrate of hemicellulose) and synergy (preference for cellulose and hemicellulose) coexisted in the bacteria-fungi interactions. In conclusion, these findings provide useful information for understanding the biodegradation of tomato plant residues better, and effects of the functional agents identified on composting process should be further studied.

A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species

The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.

Effects of microbial floras on the distributions of five domestic Drosophila species across fruit resources

The distributions of five Drosophila species and four components of the microflora have been compared across a total of 48 traps baited with four different fruit and vegetable substrates in two domestic compost heaps in Canberra (Australia). Large and consistent differences are found, both among the Drosophila and among the microbial classes, in their distributions across traps baited with different substrates. Moreover the distribution of each Drosophila species shows a unique set of strong associations with the microbial distributions. Thus the distributions of both D. simulans and D. melanogaster are found to be strongly negatively correlated with the abundance of bacteria while D. simulans is also strongly positively correlated with the titre of fermenter yeasts. D. immigrans is strongly positively correlated both with bacteria and with non-fermenter yeasts. D. hydei is positively correlated with nonfermentery yeasts and D. busckii is negatively correlated with fermenter yeasts. Moulds are the only microbial class not consistently associated with the distribution of any of the Drosophila species. The correlations with the other microbial classes are sufficient to explain the majority of the abundance differences of the Drosophila species among the trap types. It is therefore proposed that the clear partitioning of the fruit resources by the Drosophila is due to their differing primary interactions with the microflora.