A fine-scale phylogenetic analysis of free-living Burkholderia species in sugarcane field soil

Obligate Gut Symbiotic Association with Caballeronia in the Mulberry Seed Bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae)

Many insects possess symbiotic bacteria in their bodies, and microbial symbionts play pivotal metabolic roles for their hosts. Members of the heteropteran superfamilies Coreoidea and Lygaeoidea stinkbugs harbor symbionts of the genus Caballeronia in their intestinal tracts. Compared with symbiotic associations in Coreoidea, those in Lygaeoidea insects are still less understood. Here, we investigated a symbiotic relationship involving the mulberry seed bug Paradieuches dissimilis (Lygaeoidea: Rhyparochromidae) using histological observations, cultivation of the symbiont, 16S rRNA gene amplicon sequencing, and infection testing of cultured symbionts. Histological observations and cultivation revealed that P. dissimilis harbors Caballeronia symbionts in the crypts of its posterior midgut. 16S rRNA gene amplicon sequencing of field-collected P. dissimilis confirmed that the genus Caballeronia is dominant in the midgut of natural populations of P. dissimilis. In addition, PCR diagnostics showed that the eggs were free of symbiotic bacteria, and hatchlings horizontally acquired the symbionts from ambient soil. Infection and rearing experiments revealed that symbiont-free aposymbiotic individuals had abnormal body color, small body size, and, strikingly, a low survival rate, wherein no individuals reached adulthood, indicating an obligate cooperative mutualism between the mulberry seed bug and Caballeronia symbionts.

Effects of Different Vegetable Rotations on Fungal Community Structure in Continuous Tomato Cropping Matrix in Greenhouse

Intensive greenhouse vegetable cultivation aggravates continuous cropping, resulting in the disturbance of the microbial community structure and the diversity of the soil matrix. In this study, we evaluated the diversity of the rhizosphere matrix fungi in rotation and continuous cropping systems by using high-throughput sequencing analysis of substrates under 6-years of continuous tomato cropping and rotation with cabbage, bean, or celery in greenhouse pots. The results showed that fungal richness in the Chinese cabbage rotation treatment (B) was significantly lower than that of other treatments, and fungal diversities of treatment B and the bean rotation treatment (D) were significantly lower than that of continuous tomato cropping (CK). Contrastingly, the celery rotation treatment (Q) increased the fungal diversity and richness. Furthermore, a principal coordinate analysis showed that the fungal soil community structure of each rotation treatment was different from that of CK. The relative abundances of several harmful fungi (such as Pseudogymnoascus, Gibberella, and Pyrenochaeta) in control CK were significantly higher than those in rotation treatments. In addition, the matrix electrical conductivity, organic matter, total K, and available P in treatments B and D were significantly higher than those in control CK. Moreover, pH and total N of treatment Q were significantly higher than those of control CK. Most fungi were positively correlated with organic matter and available P and negatively correlated with pH. Therefore, rotation with celery could improve the abundance and diversity of fungi in continuous tomato cropping substrates and reduce the relative abundance of harmful fungi. These results indicated that the rotation of celery and tomato could effectively maintain the ecological balance of the substrate microenvironment and provide a more effective way to prevent the problems of continuous tomato cropping in greenhouse.

Host-symbiont specificity determined by microbe-microbe competition in an insect gut

Despite the omnipresence of specific host-symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the specificity of the interaction evolved and is maintained. The bean bug Riptortus pedestris acquires a specific bacterial symbiont of the genus Burkholderia from environmental soil and harbors it in midgut crypts. The genus Burkholderia consists of over 100 species, showing ecologically diverse lifestyles, and including serious human pathogens, plant pathogens, and nodule-forming plant mutualists, as well as insect mutualists. Through infection tests of 34 Burkholderia species and 18 taxonomically diverse bacterial species, we demonstrate here that nonsymbiotic Burkholderia and even its outgroup Pandoraea could stably colonize the gut symbiotic organ and provide beneficial effects to the bean bug when inoculated on aposymbiotic hosts. However, coinoculation revealed that the native symbiont always outcompeted the nonnative bacteria inside the gut symbiotic organ, explaining the predominance of the native Burkholderia symbiont in natural bean bug populations. Hence, the abilities for colonization and cooperation, usually thought of as specific traits of mutualists, are not unique to the native Burkholderia symbiont but, to the contrary, competitiveness inside the gut is a derived trait of the native symbiont lineage only and was thus critical in the evolution of the insect gut symbiont.

Burkholderia Gut Symbionts Associated with European and Japanese Populations of the Dock Bug Coreus marginatus (Coreoidea: Coreidae)

Insects of the heteropteran superfamilies Coreoidea and Lygaeoidea are consistently associated with symbionts of a specific group of the genus Burkholderia, called the “stinkbug-associated beneficial and environmental (SBE)” group. The symbiosis is maintained by the environmental transmission of symbionts. We investigated European and Japanese populations of the dock bug Coreus marginatus (Coreoidea: Coreidae). High nymphal mortality in reared aposymbiotic insects suggested an obligate host-symbiont association in this species. Molecular phylogenetic analyses based on 16S rRNA gene sequences revealed that all 173 individuals investigated were colonized by Burkholderia, which were further assigned to different subgroups of the SBE in a region-dependent pattern.

A selective genome-guided method for environmental Burkholderia isolation

The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMART protocol, we have developed a two-stage isolation protocol for strains from the genus Burkholderia. This method uses a combination of selective agar isolation media and multiplexed PCR profiling to derive Burkholderia strains from environmental samples with 95% efficiency. Creation of this new method paves the way for the systematic exploration of natural products chemistry from this important genus and offers new insight into potential methods for selective isolation method development for other priority genera.

Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

Soil Microbial Community Structure and Diversity around the Aging Oil Sludge in Yellow River Delta as Determined by High-Throughput Sequencing

Microorganisms are sensitive indicators of edaphic environmental variation. The Illumina MiSeq sequencing technology was used to analyze soil bacterial community diversity around an aging oil sludge in the Yellow River Delta. The alpha diversity index of soil bacterial community results (Ace, Chao, Shannon, and Simpson) determined that bacterial community diversity sampling within the scope of a 20 cm radius from the center of an aging oil sludge spot showed the most abundant diversity. The level of diversity distributed symmetrically with radial direction from the center of the aging oil sludge spot. Over the distance of 100 m from the center, bacterial community diversity tends to be monotonous, with small differences especially in the horizontal direction underground. The alpha-diversity indicators also showed that the bacterial diversity of samples were close under the aging oil sludge. In addition, the aging oil sludge inhibited the growth of bacteria compared with the referenced unpolluted soil sample and also increased the diversities of soil bacteria. At the phylum level, the Proteobacteria, Chloroflexi, and Actinobacteria existing in the aging oil sludge-contaminated wetland soil constituted a larger proportion of the community, while the proportion of Firmicute was relatively less. On the contrary, Firmicute showed the highest content of 63.8% in the referenced soil. Under the genus level and family level, the corresponding strains that resisted the aging oil sludge were selected. According to the bacterial diversity analysis, the basic structure of the bacterial community which could be used for remediation of aging oil sludge-contaminated soil was also developed.

Microbial diversity in two traditional bacterial douchi from Gansu province in northwest China using Illumina sequencing

Douchi has been consumed as a flavoring ingredient for centuries. During production of douchi, numerous microorganisms play important roles in the hydrolysis and conversion of proteins and starch, which are related to the quality and flavor of the end product. Therefore, in the present study, the microbial diversity in two types of home-made traditional bacterial douchi from Gansu province in northwest China was studied by high-throughput sequencing, and a corresponding analysis of the bacterial and fungal communities were conducted. The results showed that geography may have impacted the fungal diversity and the bacterial and fungal species richness in the samples. The results also showed that the microbial community was significantly different in samples of different origin and the difference in the microbial community at the genus level was greater than at phylum level. Two dominant bacterial genera (Bacillus and Ignatzschineria) were common to the two samples, both of which had a relative abundance of more than 1%. Four bacterial genera (Staphylococcus, Aerococcus, Geobacillus, and Jeotgalicoccus) were dominant only in the sample from Qingyang, while another four (Carnobacterium, Proteus, Aneurinibacillus, and Enterococcus) were dominant only in the sample from Longnan. Two dominant fungal genera (Pichia and Candida) were shared by the two samples. Additionally, two genera (Rhodosporidium and Yarrowia) were dominant only in samples from Longnan. The functional genes of the bacteria present in samples indicated that a significant difference was observed in the bacterial community between samples of different origin. We also found that microbial interactions between bacterial and fungal communities in the samples were very complex. This study provides previously unknown information regarding the impact of the environment on microbial communities in douchi and lays a foundation for further investigations into food ecology in bacterial douchi.

Effects of different carriers on biogas production and microbial community structure during anaerobic digestion of cassava ethanol wastewater

In this study, an anaerobic bioreactor (AB) with no added fillers (ABWF), a packed-bed bioreactor with a porous ceramic filler (ABCF), and another packed-bed bioreactor filled with graphite felt (ABGF) were established for anaerobic digestion of cassava ethanol wastewater. The results showed that ABCF exhibited excellent wastewater treatment performance in a stable process that was superior to ABWF and ABGF, with the following characteristics: a high chemical oxygen demand removal efficiency of 98.06% and maximum biogas production of 3200 mL/d at a total reactor volume of 3.46 L. Illumina MiSeq sequencing analysis revealed that differences existed among the microbial communities of the three ABs that were in accordance with the operational characteristics. The ABCF system displayed maximum bacterial diversity, whereas the ABWF system exhibited moderate richness and the ABGF system possessed the lowest species richness. The ABCF system was more stable than the ABWF and ABGF systems during anaerobic digestion of cassava ethanol wastewater. Different functional microbial communities that are responsible for the degradation of certain compounds were also identified in the ABCF and ABGF systems. Our results demonstrate that ceramic materials should be considered an appropriate support for the immobilization of cells.

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac

The bacterial community and diversity in healthy and diseased konjac rhizosphere soils with different ages of continuous cropping were investigated using next-generation sequencing. The results demonstrated that the number of years of continuous cropping significantly altered soil bacterial community and diversity. Soil bacterial Shannon diversity index and Chao 1 index decreased with the increasing cropping years of konjac. After 1 year of cropping, the soil exhibited the highest bacterial relative abundance and diversity. Of the 44 bacterial genera (relative abundance ratio of genera greater than 0.3%), 14 were significantly affected by the duration of continuous cropping and plant status. With increasing continuous cropping, Alicyclobacillus decreased, while Achromobacter, Lactobacillus, Kaistobacter, Rhodoplanes increased after 3 years continuous cropping. Continuous cropping altered the structure and composition of the soil bacterial community, which led to the reduction in the beneficial bacteria and multiplication of harmful bacteria. These results will improve our understanding of soil microbial community regulation and soil health maintenance in konjac farm systems.

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

Culturing and Characterization of Gut Symbiont Burkholderia spp. from the Southern Chinch Bug, Blissus insularis (Hemiptera: Blissidae)

The phloem-feeding Southern chinch bug, Blissus insularis, harbors a high density of the exocellular bacterial symbiont Burkholderia in the lumen of specialized midgut crypts. Here we developed an organ culture method that initially involved incubating the B. insularis crypts in osmotically balanced insect cell culture medium. This approach enabled the crypt-inhabiting Burkholderia spp. to make a transition to an in vitro environment and to be subsequently cultured in standard bacteriological media. Examinations using ribotyping and BOX-PCR fingerprinting techniques demonstrated that most in vitro-produced bacterial cultures were identical to their crypt-inhabiting Burkholderia counterparts. Genomic and physiological analyses of gut-symbiotic Burkholderia spp. that were isolated individually from two separate B. insularis laboratory colonies revealed that the majority of individual insects harbored a single Burkholderia ribotype in their midgut crypts, resulting in a diverse Burkholderia community within each colony. The diversity was also exhibited by the phenotypic and genotypic characteristics of these Burkholderia cultures. Access to cultures of crypt-inhabiting bacteria provides an opportunity to investigate the interaction between symbiotic Burkholderia spp. and the B. insularis host. Furthermore, the culturing method provides an alternative strategy for establishing in vitro cultures of other fastidious insect-associated bacterial symbionts.

IMPORTANCE

An organ culture method was developed to establish in vitro cultures of a fastidious Burkholderia symbiont associated with the midgut crypts of the Southern chinch bug, Blissus insularis The identities of the resulting cultures were confirmed using the genomic and physiological features of Burkholderia cultures isolated from B. insularis crypts, showing that host insects maintained the diversity of Burkholderia spp. over multiple generations. The availability of characterized gut-symbiotic Burkholderia cultures provides a resource for genetic manipulation of these bacteria and for examination of the mechanisms underlying insect-bacterium symbiosis.

Members of the genus Burkholderia: good and bad guys

In the 1990s several biocontrol agents on that contained Burkholderia strains were registered by the United States Environmental Protection Agency (EPA). After risk assessment these products were withdrawn from the market and a moratorium was placed on the registration of Burkholderia-containing products, as these strains may pose a risk to human health. However, over the past few years the number of novel Burkholderia species that exhibit plant-beneficial properties and are normally not isolated from infected patients has increased tremendously. In this commentary we wish to summarize recent efforts that aim at discerning pathogenic from beneficial Burkholderia strains.

High throughput sequencing analysis of the joint effects of BDE209-Pb on soil bacterial community structure

Decabromodiphenyl ether (BDE209) and Lead (Pb) are the main pollutants at e-waste recycling sites (EWRSs). However, the impact on soil microorganism of joint exposure to the two chemicals remains almost unknown. Therefore, the indoor incubation tests were performed to determine the response of soil microbial biomass and activity as well as bacterial community structure in the presence of the two chemicals during 60 d incubation period. The results indicated that after Pb alone or BDE209-Pb exposure, soil microbial biomass C (Cmic) was significantly lower (p<0.01), and soil basal respiration (SBR) and metabolic quotient (qCO2) were enhanced, while BDE209 barely resulted in significant influence (p>0.05). 16S rRNA gene sequencing on the Illumina MiSeq platform demonstrated that a total 49,405 valid sequences widely represented the diversity of microbial community. Sequence analyses at phylum and genus taxonomic levels illustrated that 11 identified phyla and 297 genera were observed among all the soil samples, and the contaminants input had affected bacterial community structure, suggesting that Proteobacteria, Actinobacteria and Acidobacteria were the dominant phyla, and the genera Massilia and Bacillus were enriched in contaminated soil. BDE209 exposure alone in all the samples indicated a more similar community structure compared to the control. The results of these observations have provided a better understanding of ecotoxicological effects of BDE209 and Pb joint exposure on indigenous microorganisms in soil at EWRSs.

Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing

This study was carried out to understand microbial diversity and function in the microbial enhanced oil recovery (MEOR) process and to assess the impact of MEOR treatment on the microbial community in an oil reservoir. The Illumina MiSeq-based method was used to investigate the structure and dynamics of the microbial community in a MEOR-treated block of the Baolige oilfield, China. The results showed that microbial diversity was high and that 23 phyla occurred in the analyzed samples. Proteobacteria, Firmicutes, Bacteroidetes, Thermotogae, and Euryarchaeota were present in relatively high abundance in all analyzed samples. Injection of bacteria and nutrients resulted in interesting changes in the composition of the microbial community. During MEOR treatment, the community was dominated by the known hydrocarbon-utilizing genera Pseudomonas and Acinetobacter. After the treatment, the two genera decreased in abundance over time while Methanobacteriaceae, as well as known syntrophic genera such as Syntrophomonas, Pelotomaculum, Desulfotomaculum, and Thermacetogenium gradually increased. The change in dominant microbial populations indicated the presence of a succession of microbial communities over time, and the hydrocarbon degradation and syntrophic oxidation of acetate and propionate to methane in the MEOR-treated oilfield. This work contributes to a better understanding of microbial processes in oil reservoirs and helps to optimize MEOR technology.

Insecticide applications to soil contribute to the development of Burkholderia mediating insecticide resistance in stinkbugs

Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e. symbiotic and nonsymbiotic fenitrothion degraders and nondegraders) in fenitrothion-treated soil using microcosms. During the incubation with five applications of pesticide, the density of the degraders increased from less than the detection limit to around 10(6)/g of soil. The number of dominant species among the degraders declined with the increasing density of degraders; eventually, one species predominated. This process can be explained according to the competitive exclusion principle using V(max) and K(m) values for fenitrothion metabolism by the degraders. We performed a phylogenetic analysis of representative strains isolated from the microcosms and evaluated their ability to establish symbiosis with the stinkbug Riptortus pedestris. The strains that established symbiosis with R. pedestris were assigned to a cluster including symbionts commonly isolated from stinkbugs. The strains outside the cluster could not necessarily associate with the host. The degraders in the cluster predominated during the initial phase of degrader dynamics in the soil. Therefore, only a few applications of fenitrothion could allow symbiotic degraders to associate with their hosts and may cause the emergence of symbiont-mediated insecticide resistance.