Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

A combination of Sanger and 454 sequences of small subunit rRNA loci were used to interrogate microbial diversity in the bovine rumen of 12 cows consuming a forage diet. Observed bacterial species richness, based on the V1–V3 region of the 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales, Erysipelotrichales and unclassified TM7. Abundance of Prevotella species varied widely among the 12 animals. Archaeal species richness, also based on 16S rRNA, was between 8 and 13 OTUs, representing 5 genera. The majority of archaeal OTUs (84%) found in this study were previously observed in public databases with only two new OTUs discovered. Observed rumen fungal species richness, based on the 18S rRNA gene, was between 21 and 40 OTUs with 98.4–99.9% of OTUs represented by more than one read, using Good’s coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while Butyrivibrio and Blautia were significantly overrepresented in the solid fraction of the rumen. No statistical difference was observed between the liquid and solid fractions in biodiversity of archaea and fungi. The survey of microbial communities and analysis of cross-domain correlations suggested there is a far greater extent of microbial diversity in the bovine rumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understand how rumen microbial community structure and function affects ruminant feed efficiency, biofuel production, and environmental impact.     

Cloacal microbial communities of female spotted towhees Pipilo maculatus: microgeographic variation and individual sources of variability

We used Polymerase Chain Reaction (PCR) amplification of 16S rRNA genes and Denaturing Gradient Gel Electrophoresis (DGGE) to describe the microbial communities present in the cloacae of spotted towhees Pipilo maculatus. Our goals were to quantify bacterial diversity of breeding females, describe microgeographic variation of cloacal communities in a network of four urban parks in Portland, OR, and evaluate the degree to which microbial species richness varied with individual female characteristics (age, size, and condition). We detected 57 Operational Taxonomic Units (OTUs) in 46 towhees, but most OTUs showed a relatively low prevalence. Discriminant function analysis correctly classified 69.6% of towhees to their park of origin based on the presence or absence of five OTUs. Parks thus had unique “microbial signatures”. The presence or absence of specific OTUs was not associated with a female's age, but a general linear models analysis established that OTU richness was greatest among females with short tails, narrow bills, and with the exception of one individual, among relatively heavy birds. We speculate that the microgeographic differences in cloacal microbial community structure may exist due to differences in anthropogenic influences among parks. The explanations for the negative relationship between microbial richness and flight feather length, but positive relationship between microbial richness and body condition are unclear, but may reflect the different time frames over which feather growth and body mass are determined.     

Dosage-dependent shift in the spore community of arbuscular mycorrhizal fungi following application of tannery sludge

The controlled disposal of tannery sludge in agricultural soils is a viable alternative for recycling such waste; however, the impact of this practice on the arbuscular mycorrhizal fungi (AMF) communities is not well understood. We studied the effects of low-chromium tannery sludge amendment in soils on AMF spore density, species richness and diversity, and root colonization levels. Sludge was applied at four doses to an agricultural field in Rolandia, Paraná state, Brazil. The sludge was left undisturbed on the soil surface and then the area was harrowed and planted with corn. The soil was sampled at four intervals and corn roots once within a year (2007/2008). AMF spore density was low (1 to 49 spores per 50 cm³ of soil) and decreased as doses of tannery sludge increased. AMF root colonization was high (64%) and unaffected by tannery sludge. Eighteen AMF species belonging to six genera (Acaulospora, Glomus, Gigaspora, Scutellospora, Paraglomus, and Ambispora) were recorded. At the sludge doses of 9.0 and 22.6 Mg ha⁻¹, we observed a decrease in AMF species richness and diversity, and changes in their relative frequencies. Hierarchical grouping analysis showed that adding tannery waste to the soil altered AMF spore community in relation to the control, modifying the mycorrhizal status of soil and selectively favoring the sporulation of certain species.     

Gamma radiation effects on growth and yield attributes of <Emphasis Type="Italic">Psoralea corylifolia</Emphasis> L. with reference to enhanced production of psoralen

The present work describes radiation-induced effects on vegetative, reproductive traits and psoralen content in Psoralea corylifolia L. The effects of gamma radiation on Psoralea seeds were investigated by exposing seeds with doses of 2.5, 5, 10, 15 and 20 kGy at dose rate of 1.65 kGyh⁻¹ and studying the plant growth at three developmental stages: preflowering, flowering and post flowering (seed to seed) after irradiation. Irradiation with lower doses of gamma rays significantly improved vegetative traits while higher doses proved depressing for same parameters. Similar trend was followed in reproductive traits. Psoralen, showed highest concentration in seeds (7.56%) at 20 kGy and lowest in control roots (0.23%). Increment in psoralen was striking for higher gamma doses applied. These long-term changes in plant development may be attributed to alteration in plant genome induced by irradiation. The results show in depth development stimulation and enhancement of secondary metabolite in Psoralea corylifolia L. following low and high dose treatment respectively depicting the potential of gamma rays in plant biotechnology and metabolomics.     

Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.     

Effect of gamma irradiation on microbial load,aflatoxins and phytochemicals present in Trigonella foenum-graecum

The effects of gamma irradiation on microbial load, total aflatoxins and phytoconstituents content of Trigonella foenum-graecum have been studied. Gamma irradiation at a dose of 2.5 kGy resulted in 2 log reduction of the total aerobic microbial count. A complete sterilization was, however, observed at 10 kGy. The total aflatoxin level decreased gradually with increase in gamma irradiation dose as compared to its un-irradiated counterparts, whereas the high performance liquid chromatography (HPLC) profile showed no change in the levels of phytochemicals up to the gamma irradiation dose of 10 kGy. HPLC profiles, however, differed in peak areas, and retention times of the components. These results suggest that gamma irradiation at a dose of 5.0 kGy was very effective for microbial decontamination because it did not adversely affect the active components of T. foenum-graecum.     

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.     

Nitrogen and phosphorus additions impact arbuscular mycorrhizal abundance and molecular diversity in a tropical montane forest

Increased nitrogen (N) depositions expected in the future endanger the diversity and stability of ecosystems primarily limited by N, but also often co‐limited by other nutrients like phosphorus (P). In this context a nutrient manipulation experiment (NUMEX) was set up in a tropical montane rainforest in southern Ecuador, an area identified as biodiversity hotspot. We examined impacts of elevated N and P availability on arbuscular mycorrhizal fungi (AMF), a group of obligate biotrophic plant symbionts with an important role in soil nutrient cycles. We tested the hypothesis that increased nutrient availability will reduce AMF abundance, reduce species richness and shift the AMF community toward lineages previously shown to be favored by fertilized conditions. NUMEX was designed as a full factorial randomized block design. Soil cores were taken after 2 years of nutrient additions in plots located at 2000 m above sea level. Roots were extracted and intraradical AMF abundance determined microscopically; the AMF community was analyzed by 454‐pyrosequencing targeting the large subunit rDNA. We identified 74 operational taxonomic units (OTUs) with a large proportion of Diversisporales. N additions provoked a significant decrease in intraradical abundance, whereas AMF richness was reduced significantly by N and P additions, with the strongest effect in the combined treatment (39% fewer OTUs), mainly influencing rare species. We identified a differential effect on phylogenetic groups, with Diversisporales richness mainly reduced by N additions in contrast to Glomerales highly significantly affected solely by P. Regarding AMF community structure, we observed a compositional shift when analyzing presence/absence data following P additions. In conclusion, N and P additions in this ecosystem affect AMF abundance, but especially AMF species richness; these changes might influence plant community composition and productivity and by that various ecosystem processes.     

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75‐m depth. The communities of microbial eukaryotes were clustered into shallow‐, middle‐, and deep‐water groups according to the depth from which they were collected, indicating a depth‐related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50‐m deep, being most abundant near the sea floor where they contributed ca. 64–97% and 40–74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area.     

Defining seasonal marine microbial community dynamics

Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.     

Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0–30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.     

Ribosomal Tag Pyrosequencing of DNA and RNA Reveals “Rare” Taxa with High Protein Synthesis Potential in the Sediment of a Hypersaline Lake in Western Australia

Little is known about the potential activity of microbial communities in hypersaline sediment ecosystems. Ribosomal tag libraries of DNA and RNA extracted from the sediment of Lake Strawbridge (Western Australia) revealed bacterial and archaeal operational taxonomic units (OTUs) with high RNA/DNA ratios providing evidence for the presence of ‘rare’ but potentially “active” taxa. Among the ‘rare’ bacterial taxa Halomonas, Salinivibrio and Idiomarina showed the highest protein synthesis potential. Rare but ‘active’ archaeal OTUs were related to the KTK 4A cluster and the Marine-Benthic-Groups B and D. We present the first molecular analysis of the microbial diversity and protein synthesis potential of rare microbial taxa in a hypersaline sediment ecosystem.     

Fungal diversity and functionality are driven by soil texture in Taylor Valley,Antarctica

The McMurdo Dry Valleys surface is mainly constituted from unconsolidated permafrost. Despite the combination of cold and dry conditions, transiently wetted soils close to lake edges are hotspots of intense biological activity, that can support the surrounding soil ecosystems in such extreme environments. These soils host simple microbial communities that allow easy characterization of the parameters determining microbial establishment and diversification. Soil samples were collected close to three different glacial lakes (Lake Fryxell, Lake Hoare and Lake Joyce) located along a longitudinal gradient from the lower to the upper Taylor Valley. Fungal diversity and functionality of sampled soils were studied through ITS1 metabarcoding sequencing. The correlation between the parameters describing fungal diversity (i.e. total richness, relative richness of dominant taxonomic and functional groups, and community composition) and the edaphic physicochemical parameters (i.e. pH, moisture, C, N, P, Na⁺, K⁺, Mg²⁺ and Ca²⁺, cation exchange capacity, and soil granulometry) was assessed. The fungal communities showed low richness (48 ± 32 OTUs per sample). Their composition was highly diversified even within different sites close to the same lake. The main parameters affecting the diversity and composition of fungal communities were soil texture, in turn influencing the retention of water and nutrients, and physicochemical properties. This is of particular concern for the survival of these communities, given the expected environmental changes due to global warming.     

Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia

Photosynthetic microbial communities under translucent rocks (hypolithic) are found in many arid regions. At the global scale, there has been little intercontinental gene flow, and at a local scale, microbial composition is related to fine‐scale features of the rocks and their environment. Few studies have investigated patterns of hypolithic community composition at intermediate distances. We examined hypolithic cyanobacterial diversity in semi‐arid Australia along a 10‐km transect by sampling six rocks from four adjacent 1 m² quadrats (“distance zero”) and from additional quadrats at 10, 100, 1,000, and 10,000 m to test the hypothesis that diversity would increase with the number of rocks sampled and distance. A total of 3,108 cyanobacterial operational taxonomic units (OTUs) were detected. Most were neither widespread nor abundant. The few that were widespread tended to be abundant. There was no difference in the community composition between the four sites at distance zero, but the samples 10 m away were significantly different, as were those at all other distances compared to distance zero. Many additional OTUs were recorded with increasing distance up to 100 m. These patterns of distribution are consistent with a colonization model involving dispersal from rock to rock. Our results indicate that distance was a significant factor that can be confounded by interrock differences. Most diversity was represented in the first 100 m of the transect, with an additional 1.5% of the total diversity added by the sample at 1 km, but only 0.2% added with the addition of the 10‐km site.     

基于高通量测序的辐射污染区细菌群落特征分析

【目的】为了更加全面地揭示辐射污染区细菌种群多样性,了解辐射污染对辐射区土壤中细菌群落结构的影响。【方法】运用高通量测序方法,分别进行了土样细菌16S r RNA基因的V3可变区测序,进而对无辐射污染对照和不同辐射污染程度的土样中细菌群落组成和多样性进行分析。【结果】研究共获得110 348条有效序列,17 604个OTUs,共涉及细菌域的19个门和6个潜在菌门和其它未分类菌群的726个属。多样性分析表明,辐射污染会引起土壤样品中微生物群落的分布显著差异化,显著提高细菌群落种群多样性和微生物丰度。微生物群落组成分析发现,在辐射污染胁迫下,辐射污染区样品中变形杆菌门分布比例显著下降;随着辐射污染程度的提高,放线菌门所占比例逐步提高,未分类菌门、厚壁菌门和酸杆菌门也有明显的提高。同时,研究发现辐射污染区中存在着大量未分类菌属。【结论】研究揭示了辐射污染区极为丰富的细菌多样性,大量微生物新物种资源有待发掘。     

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre

Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0–1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology‐based studies in the region (4,024 OTUs, 10‐fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic–upper mesopelagic depths (100–300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth‐stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2–0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.     

Microbial load, acidity, lipid oxidation and volatile basic nitrogen of irradiated fish and meat-bone meals

Experiments were carried out to study the effect of different doses of gamma irradiation (0, 5, 10, 15 and 20 kilo gray; kGy) on some nutritive components and chemical aspects pertaining to quality of fish meal and meat-bone meal. The radiation doses required to reduce the total microbial load and Salmonella sp. one log cycle (D(10)) in fish meal and meat-bone meal were determined. Results indicated that gamma irradiation of fish meal and meat-bone meal with 5-20 kGy doses had no effects on the total acidity values but increased the values of lipid oxidation and total volatile basic nitrogen. D(10) of total microbial load and Salmonella sp. were 833 and 313 Gy for fish meal and 526 Gy and 278 Gy for meat-bone meal, respectively. It can be concluded that radiation processing could be employed in the recycling of fish and meat-bone meals by using them as feedstuffs in poultry diets with no fear of losing their nutritive components.     

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

Rare taxa overwhelm metabarcoding data generated using next-generation sequencing (NGS). Low frequency Operational Taxonomic Units (OTUs) may be artifacts generated by PCR-amplification errors resulting from polymerase mispairing. We analyzed two Internal Transcribed Spacer 2 (ITS2) MiSeq libraries generated with proofreading (ThermoScientific Phusion^®) and non-proofreading (ThermoScientific Phire^®) polymerases from the same MiSeq reaction, the same samples, using the same DNA tags, and with two different clustering methods to evaluate the effect of polymerase and clustering tool choices on the estimates of richness, diversity and community composition. Our data show that, while the overall communities are comparable, OTU richness is exaggerated by the use of the non-proofreading polymerase–up to 15 % depending on the clustering method, and on the threshold of low frequency OTU removal. The overestimation of richness also consistently led to underestimation of community evenness, a result of increase in the low frequency OTUs. Stringent thresholds of eliminating the rare reads remedy this issue; exclusion of reads that occurred ≤10 times reduced overestimated OTU numbers to <0.3 %. As a result of these findings, we strongly recommend the use of proofreading polymerases to improve the data integrity as well as the use of stringent culling thresholds for rare sequences to minimize overestimation of community richness.     

Change in Bacterial Community Structure in Response to Disturbance of Natural Hardwood and Secondary Coniferous Forest Soils in Central Taiwan

Forest management often results in changes in the soil and its microbial communities. In the present study, differences in the soil bacterial community caused by forest management practices were characterized using small subunit (SSU) ribosomal RNA (rRNA) gene clone libraries. The communities were from a native hardwood forest (HWD) and two adjacent conifer plantations in a low-elevation montane, subtropical experimental forest at the Lienhuachi Experimental Forest (LHCEF) in central Taiwan. At this locality, the elevation ranges from 600 to 950 m, the mean annual precipitation is 2,200 mm, the mean annual temperature is 20.8°C, and the soil pH is 4. The conifer forests included a Cunninghamia konishii Hay (CNH) plantation of 40 years and an old growth Calocedrus formosana (Florin) Florin (CLC) forest of 80 years. A total of 476 clones were sequenced and assigned into 12 phylogenetic groups. Proteobacteria-affiliated clones (53%) predominated in the library from HWD soils. In contrast, Acidobacteria was the most abundant phylum and comprised 39% and 57% in the CLC and CNH libraries, respectively. Similarly, the most abundant OTUs in HWD soils were greatly reduced or absent in the CLC and CNH soils. Based on several diversity indices, the numbers of abundant OTUs and singletons, and rarefaction curves, the diversity of the HWD community (0.95 in evenness and Shannon diversity indices) was somewhat less than that in the CNH soils (0.97 in evenness and Shannon diversity indices). The diversity of the community in CLC soils was intermediate. The differences in diversity among the three communities may also reflect changes in abundances of a few OTUs. The CNH forest soil community may be still in a successional phase that is only partially stabilized after 40 years. Analysis of molecular variance also revealed that the bacterial community composition of HWD soils was significantly different from CLC and CNH soils (p = 0.001). These results suggest that the disturbance of forest conversion and tree species composition are important factors influencing the soil bacterial community among three forest ecosystems in the same climate.     

Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China

Tobacco-rice rotation is a common farming system in south China, and many tillage practices such as straw mulching, dolomite dust, and quicklime application have been adopted to improve crop production. These agricultural management practices alter soil physical and chemical properties and affect microbial life environment and community composition. In this research, six tillage practices including no tobacco and rice straw mulching (CK), tobacco and rice straw mulching (TrSr), rice straw returning fire (TrSc), tobacco and rice straw mulching with dolomite dust (TSD), rice straw returning fire and quicklime (TSQ), and rice straw returning fire, quicklime and reduced fertilizer (TSQf) were conducted to detect changes in soil bacterial diversity and composition using Illumina sequencing. The results showed that the total number of operational taxonomic units (OTUs) from the six treatments was 2030, and the number of mutual OTUs among all samples was 550. The TrSc treatment had the highest diversity and richness, while TSQf had the lowest. Soil physio-chemical properties and microbial diversity can influence each other. Proteobacteria and Actinobacteria had the greatest proportion in all treatments. The abundance of Nitrospirae was the highest in the TrSc treatment. The TSQf treatment had the highest abundance of Firmicutes. The abundance of Nitrospira in the TrSc treatment was 2.29-fold over CK. Streptomyces affiliated with Firmicutes improved by 37.33% in TSQf compared to TSQ. TSQf treatment was considered to be the most important factor in determining the relative abundance at the genus level.