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Bacteria and fungi are core microorganisms in diverse ecosystems, and their cross‐kingdom interactions are considered key determinants of microbiome structure and ecosystem functioning. However, how bacterial‐fungal interactions mediate soil organic carbon (SOC) dynamics remains largely unexplored in the context of artificial forest ecosystems.Here, we characterised soil bacterial and fungal communities in four successive planting of Eucalyptus and compared them to a neighbouring evergreen broadleaf forest. Carbon (C) mineralisation combined with five C‐degrading enzymatic activities was investigated to determine the effects of successive planting of Eucalyptus on SOC dynamics.Our results indicated that successive planting of Eucalyptus significantly altered the diversity and structure of soil bacterial and fungal communities and increased the negative bacterial‐fungal associations. The bacterial diversity significantly decreased in all Eucalyptus plantations compared to the evergreen forest, while the fungal diversity showed the opposite trend. The ratio of negative bacterial‐fungal associations increased with successive planting of Eucalyptus due to the decrease in SOC, ammonia nitrogen (NH4+‐N), nitrate nitrogen (NO3−‐N) and available phosphorus (AP). Structural equation modelling indicated that the potential cross‐kingdom competition, based on the ratio of negative bacterial‐fungal correlations, was significantly negatively associated with the diversity of total bacteria and keystone bacteria, thereby increasing C‐degrading enzymatic activities and C mineralisation.Synthesis and applications: Our results highlight the regulatory role of the negative bacterial‐fungal association in enhancing the correlation between bacterial diversity and C mineralisation. This suggests that promoting short‐term successive planting in the management of Eucalyptus plantations can mitigate the impact of this association on SOC decomposition. Taken together, our study advances the understanding of bacterial‐fungal negative associations to mediate carbon mineralisation in Eucalyptus plantations, giving us a new insight into SOC cycling dynamics in artificial forests. [ABSTRACT FROM AUTHOR]

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub‐communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub‐communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub‐communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils. [ABSTRACT FROM AUTHOR]

Summary: The mechanisms underlying microbial community dynamics and co‐occurrence patterns along ecological succession are crucial for understanding ecosystem recovery but remain largely unexplored. Here, we investigated community dynamics and taxa co‐occurrence patterns in bacterial and fungal communities across a well‐established chronosequence of post‐mining lands spanning 54 years of recovery. Bacterial community structures became increasingly phylogenetically clustered with soil age at early successional stages and varied less at later successional stages. The dynamics of bacterial community phylogenetic structures were determined by the changes in the soil vegetation cover along succession. The dynamics of fungal community phylogenetic structures did not significantly correlate with soil age, soil properties or vegetation cover, and were mainly attributed to stochastic processes. Along succession, the common decrease in the bacterial co‐occurrence complexity and in the average pairwise phylogenetic distances between co‐occurring bacteria implied a decrease in potential bacterial cooperation. The increased complexity of fungal co‐occurrence along succession was independent of phylogenetic relatedness between co‐occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession. [ABSTRACT FROM AUTHOR]

The size of bacterial genomes is often associated with organismal metabolic capabilities determining ecological breadth and lifestyle. The recently proposed Candidate Phyla Radiation (CPR)/Patescibacteria encompasses mostly unculturable bacterial taxa with relatively small genome sizes with potential for co‐metabolism interdependencies. As yet, little is known about the ecology and evolution of CPR, particularly with respect to how they might interact with other taxa. Here, we reconstructed two novel genomes (namely, Candidatus Saccharibacter sossegus and Candidatus Chaer renensis) of taxa belonging to the class Saccharimonadia within the CPR/Patescibacteria using metagenomes obtained from acid mine drainage (AMD). By testing the hypothesis of genome streamlining or symbiotic lifestyle, our results revealed clear signatures of gene losses in these genomes, such as those associated with de novo biosynthesis of essential amino acids, nucleotides, fatty acids and cofactors. In addition, co‐occurrence analysis provided evidence supporting potential symbioses of these organisms with Hydrotalea sp. in the AMD system. Together, our findings provide a better understanding of the ecology and evolution of CPR/Patescibacteria and highlight the importance of genome reconstruction for studying metabolic interdependencies between unculturable Saccharimonadia representatives. [ABSTRACT FROM AUTHOR]

The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (ab H08; ∼ 23%), microsomal hydrolases (ab H09; ∼ 12%) and M oraxella lipase-like proteins (ab H04 and ab H01; < 5%). Detailed analysis of the genes predicted to encode proteins of the ab H08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to A ctinobacteria, D einococcus- T hermus, P lanctomycetes and P roteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. [ABSTRACT FROM AUTHOR]

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16 S r RNA gene and internal transcribed spacer ( ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. [ABSTRACT FROM AUTHOR]

The glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, is an important vector of various strains of Xylella fastidiosa, which cause disease in a variety of economically important plants. These diseases include citrus variegated chlorosis, oleander leaf scorch and Pierce's Disease of grapevines. Symbiotic control (SC) is a new strategy that uses symbiotic endophytes as biological control agents to antagonize or displace the pathogenic strains of X. fastidiosa. Candidate endophytes for use in SC must occupy the xylem of host plants and attach to the pre-cibarium and cibarium of sharpshooter insects in order to have access to the pathogen. The study of the bacterial community of GWSS heads by isolation and denaturing gradient gel electrophoresis (DGGE) revealed the presence of species that may be suitable for use in SC. In addition, the results indicated that two important factors, insect age and choice of host plant, affect the composition of the bacterial community in GWSS heads. The main bacterial genera isolated as colonizers of GWSS heads were identified, using partial 16S rRNA gene sequencing, as Bacillus, Pseudomonas, Pedobacter and Methylobacterium, as well as the species Curtobacterium flaccumfaciens. DGGE patterns revealed a diversity of endophytic species able to colonize the GWSS head. The main genera isolated in culture were also identified using this technique. Principal component analysis (PCA) from polymerase chain reaction (PCR)-DGGE patterns indicated that the bacteria inhabiting the GWSS head are similar to those found as endophytes inside the host plants, and that insect developmental stage and preferential feeding on one host plant species over another are important factors in determining the composition of the bacterial community in the GWSS head. However, a shift in host plants for a small period of time did not cause changes in the compositions of these communities. [ABSTRACT FROM AUTHOR]