Effects of Reforestation on the Structure and Diversity of Bacterial Communities in Subtropical Low Mountain Forest Soils

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Microecological Shifts in the Rhizosphere of Perennial Large Trees and Seedlings in Continuous Cropping of Poplar

The cultivation of poplar trees is hindered by persistent cropping challenges, resulting in reduced wood productivity and increased susceptibility to soil-borne diseases. These issues primarily arise from alterations in microbial structure and the infiltration of pathogenic fungi. To investigate the impact on soil fertility, we conducted an analysis using soil samples from both perennial poplar trees and three successive generations of continuously cropped poplar trees. The quantity and community composition of bacteria and fungi in the rhizosphere were assessed using the Illumina MiSeq platform. The objective of this study is to elucidate the impact of continuous cropping challenges on soil fertility and rhizosphere microorganisms in poplar trees, thereby establishing a theoretical foundation for investigating the mechanisms underlying these challenges. The study found that the total bacteria in the BT group is 0.42 times higher than the CK group, and the total fungi is 0.33 times lower than the CK group. The BT and CK groups presented relatively similar bacterial richness and diversity, while the indices showed a significant (p < 0.05) higher fungal richness and diversity in the CK group. The fractions of Bacillus were 2.22% and 2.41% in the BT and CK groups, respectively. There was a 35.29% fraction of Inocybe in the BT group, whereas this was barely observed in the CK group. The fractions of Geopora were 26.25% and 5.99%, respectively in the BT and CK groups. Modifying the microbial community structure in soil subjected to continuous cropping is deemed as the most effective approach to mitigate the challenges associated with this agricultural practice.

A special drop: Characterising yeast isolates associated with fermented beverages produced by Australia's indigenous peoples

Way-a-linah, an alcoholic beverage produced from the fermented sap of Eucalyptus gunnii, and tuba, a fermented drink made from the syrup of Cocos nucifera fructifying bud, are two of several fermented beverages produced by Australian Aboriginal and Torres Strait people. Here we describe the characterisation of yeast isolates from samples associated with the fermentation of way-a-linah and tuba. Microbial isolates were obtained from two different geographical locations in Australia - the Central Plateau in Tasmania, and Erub Island in the Torres Strait. While Hanseniaspora species and Lachancea cidri were the most abundant species in Tasmania, Candida species were the most abundant in Erub Island. Isolates were screened for tolerance to stress conditions found during the production of fermented beverages and for enzyme activities relevant to the appearance, aroma and flavour of these beverages. Based on screening results, eight isolates were evaluated for their volatile profile during the fermentation of wort, apple juice and grape juice. Diverse volatile profiles were observed for beers, ciders and wines fermented with different isolates. These findings reveal the potential of these isolates to produce fermented beverages with unique aroma and flavour profiles and highlight the vast microbial diversity associated with fermented beverages produced by Australia's Indigenous peoples.

Effects of a Microbial Restoration Substrate on Plant Growth and Rhizosphere Microbial Community in a Continuous Cropping Poplar

In poplar cultivation, continuous cropping obstacles affect wood yield and soil-borne diseases, primarily due to structural changes in microbes and fungus infection. The bacterium Bacillus cereus BJS-1-3 has strong antagonistic properties against pathogens that were isolated from the rhizosphere soil of poplars. Poplar rhizospheres were investigated for the effects of Bacillus cereus BJS-1-3 on microbial communities. Three successive generations of soil were used to replant poplar seedlings. BJS-1-3 inoculated poplars were larger, had higher plant height and breast height diameter, and had a greater number of total and culturable bacteria than non-inoculated controls. B. cereus BJS-1-3 inoculated poplar rhizospheres were sequenced, utilizing the Illumina MiSeq platform to analyze changes in diversity and structure. The fungi abundance and diversity in the BJS-1-3 rhizosphere were significantly lower than in the control rhizosphere. In comparison to the control group, Bacillus sp. constituted 2.87% and 2.38% of the total bacterial community, while Rhizoctonia sp. constituted 2.06% and 6.00% of the total fungal community. Among the potential benefits of B. cereus BJS-1-3 in poplar cultivation is that it enhances rhizosphere microbial community structure and facilitates the growth of trees.

Effects of Forest Gaps on the Structure and Diversity of Soil Bacterial Communities in Weeping Cypress Forest Plantations

The decline in forest ecological function caused by pure forest plantations planted in the Yangtze River basin is becoming increasingly serious. To investigate this problem, we selected the local low-efficiency weeping cypress plantations for forest gap transformation. Three forest gap sizes, specifically large, medium, and small gaps, were established, and the effects of gap sizes on soil bacterial community structure and diversity in winter and summer were studied compared to no gaps (CK; control). Compared to CK, forest gaps had a significant effect on soil organic carbon (SOC) and soil total nitrogen (TN), and the highest values of SOC and soil TN under two seasons occurred in large forest gaps. The interactions of forest gap sizes and seasons had significant effects on pH, SOC, TN, and alpha diversity indices, including Simpson, Chao1, and ACE indices. Compared to winter, forest gaps significantly increased the soil bacterial community diversity indices in summer. Forest gap sizes significantly affected the composition of the bacterial community, but the composition of the dominant bacteria at the phyla and genera levels was similar. Linear discriminant effect size (LEfSe) analysis showed that there were 32 indicator bacterial species in two seasons. Co-occurrence network analysis revealed that the relationship of the soil bacterial community at the phyla level was complex, and there was a significant positive correlation among bacterial species. Soil bulk density (BD) and soil moisture (SM) significantly affected the soil bacterial alpha diversity indices. The composition of the dominant bacteria at the phyla level was significantly affected by soil microbial carbon (MBC), whereas the composition of dominant bacteria at the genera level was affected by soil hydrolysable nitrogen (AN) and the carbon/nitrogen (C/N) ratio. In this study, compared to the other forest gaps, large forest gaps were more conducive to the accumulation of soil nutrients, thus improving the structure of the soil bacterial community. Importantly, changes in the soil bacterial community structure due to gap formation may have profound effects on soil biogeochemical processes in weeping cypress forest plantations.

The Effect of the Conversion from Natural Broadleaved Forests into Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) Plantations on Soil Microbial Communities and Nitrogen Functional Genes

The conversion of forests could change soil characteristics and, in turn, impact the microbial community. However, the long-term effect of forest transformation on bacterial and archaeal composition and diversity, especially on nitrogen functional communities, is poorly understood. This study aimed to explore the response of soil bacterial and archaeal communities, as well as nitrogen functional groups, to the conversion from natural broadleaved forests to Chinese fir (Cunninghamia lanceolate (Lamb.) Hook.) plantations in subtropical China by 16S rRNA amplicon sequencing. Except for soil bulk density (BD) and ammonium nitrogen (NH4+–N) content, other soil properties all decreased with the conversion from natural forests to plantations. Alpha diversity of bacteria and archaea declined with the transformation from natural forests to plantations. The composition of bacteria and archaea was significantly different between natural forests and plantations, which could be mainly attributed to the change in the content of soil organic carbon (SOC), total nitrogen (TN), nitrate nitrogen (NO3−–N), and available phosphorus (AP). The conversion of natural forests to plantations decreased the gene copies of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nifH (nitrogen fixation function) but increased denitrification gene copies (i.e., nirS, nirK, and nosZ). In summary, our study emphasizes the long-term negative effect of the conversion from natural broadleaved forests into Chinese fir plantations on the diversity and richness of soil microbial communities, thereby deeply impacting the cycling of soil nitrogen.

Comparison of the Bulk and Rhizosphere Soil Prokaryotic Communities Between Wild and Reintroduced Manglietiastrum sinicum Plants, a Threatened Species with Extremely Small Populations

Huagaimu (Manglietiastrum sinicum) trees are critically endangered species and classified as a plant species with extremely small populations in China. Rhizospheres and bulk soils prokaryotic communities play an important role to protect and promote plants health and growth. However, the compositions and structures of prokaryotic communities in wild and reintroduced M. sinicum rhizospheres and bulk soils are still poorly understood. In the present study, prokaryotic communities in wild and reintroduced M. sinicum rhizospheres and bulk soils were compared using high-throughput sequencing. Thirty-two phyla, 76 classes, 193 orders, 296 families, and 470 genera of prokaryotes were obtained. Proteobacteria and Acidobacteria were the two most abundant phyla in all soil samples. The compositions and structures of prokaryotic communities were overall similar, and the abundance of some taxa varied significantly among soil samples. Soil prokaryotic communities were significantly affected by soil pH, total nitrogen, total phosphorus, and total potassium. Eleven of predicted functions were significantly different among the four soil groups. This study provides for the first insights into the compositions, structures, and potential functions of prokaryotic communities associated with wild and reintroduced M. sinicum rhizospheres and bulk soils, and providing a foundation for future research to help protect this endangered species.

Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii

Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.