Publications

4721

Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. “CandidatusChlorobium masyuteum” grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encodingcyc2gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe “CandidatusPseudopelobacter ferreus” is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from theGeobacteralesord. nov. While “Ca.C. masyuteum” is closely related to the photoferrotrophsC. ferroooxidansstrain KoFox andC. phaeoferrooxidansstrain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyllcwith accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day–1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.

AbstractCandidate phyla radiations (CPR), accounting for a major microbial supergroup with remarkably small genomes and reduced sizes, are widely distributed yet mostly uncultured. Limited culture and its obligate reliance upon other bacteria hindered investigation of their lifestyles. In this work we isolated a CPR bacterium, TM7i, with its host Leucobacter aridocollis J1, by combination of Emulsion, Paired Isolation and Concatenation PCR (epicPCR) detection and filtrate co-culture. Genomic profiling of TM7 genomes and microscopic investigation of TM7i-J1 symbiosis suggest the conservation of type IV pili and a pili-dependent lifestyle of TM7. Further, we observed twitching motility of TM7i mediated by pili and its role played in the interaction with its host. Our results shed a light on the lifestyle about this enigmatic bacterial radiation, which may also be adopted by other CPR organisms. The epicPCR-directed isolation method underlines high efficiency of CPR bacteria isolation and thus may be used in other symbiotic or epibiotic microorganisms.

Abstract A new distribution map is provided for Candidatus Liberibacter asiaticus Jagoueix et al. Alphaproteobacteria: Rhizobiales: Rhizobiaceae. Hosts: Citrus spp. Information is given on the geographical distribution in Africa (Egypt, Ethiopia, Kenya, Mauritius, Réunion, Tanzania, Uganda), Asia (Bangladesh, Bhutan, Borneo, Cambodia, China, Fujian, Guangdong, Guangxi, Guizhou, Hainan, Hunan, Jiangxi, Sichuan, Yunnan, Zhejiang, Hong Kong, India, Andhra Pradesh, Arunachal Pradesh, Assam, Bihar, Delhi, Gujarat, Haryana, Himachal Pradesh, Jammu and Kashmir, Karnataka, Kerala, Madhya Pradesh, Maharashtra, Manipur, Meghalaya, Mizoram, Nagaland, Odisha, Punjab, Rajasthan, Sikkim, Tamil Nadu, Tripura, Uttar Pradesh, Uttarakhand, West Bengal, Indonesia, Java, Lesser Sunda Islands, Provinsi Papua, Sulawesi, Sumatra, Iran, Japan, Kyushu, Ryukyu Islands, Laos, Malaysia, Peninsular Malaysia, Sarawak, Myanmar, Nepal, Oman, Pakistan, Philippines, Saudi Arabia, Sri Lanka, Taiwan, Thailand, Vietnam, Yemen), North America (Barbados, Belize, Costa Rica, Cuba, Dominica, Dominican Republic, Guadeloupe, Guatemala, Honduras, Jamaica, Martinique, Mexico, Nicaragua, Panama, Puerto Rico, Trinidad and Tobago, Unites States Virgin Islands, USA, Alabama, California, Florida, Georgia, Louisiana, South Carolina, Texas), Oceania (Papua New Guinea, Timor Leste), South America (Argentina, Brazil, Bahia, Minas Gerais, Paraná, São Paulo, Colombia, Paraguay, Venezuela).

Bactericera cockerelli es una plaga de importancia económica en solanáceas en México, por los amarillamientos que causa en los cultivos, así como por la transmisión de Candidatus Liberibacter solanacearum. Se describen variantes genéticas de este insecto, las cuales se relacionan con su capacidad para fungir como vector. En México, la distribución de B. cockerelli es muy amplia y se carece de información acerca de sus características morfológicas y genéticas. El objetivo de esta investigación fue caracterizar morfológica y genéticamente a B. cockerelli y detectar la presencia de Ca. L. solanacearum en poblaciones de B. cockerelli de las zonas productoras de solanáceas en México. Para lo cual se muestrearon 35 localidades de 13 estados, sobre cultivos de chile, tomate, berenjena y papa, bajo diferentes sistemas de producción. Se midieron las variables largas de cuerpo (LC), largas de abdomen (LAB) y ancho de abdomen (AAB) en insectos de cada población, se detectó la presencia de Ca. L. solanacearum en los 13 estados muestreados, donde los machos presentaron el mayor porcentaje de insectos positivos. La presencia de Ca. L. solanacearum no se vio influenciada por el hospedero o el sistema de producción, sino por la presencia de B. cockerelli.

Citrus Huanglongbing (HLB; yellow shoot disease) is associated with an unculturable α-proteobacterium “Candidatus Liberibacter asiaticus” (CLas). HLB was found in southern California in 2012, and the current management strategy is based on suppression of the Asian citrus psyllid (Diaphorina citri) that transmits CLas and removal of confirmed CLas-positive trees. Little is known about Asian citrus psyllid-associated bacteria and citrus-associated bacteria in the HLB system. Such information is important in HLB management, particularly for accurate detection of CLas. Recent advancements in next-generation sequencing technology provide new opportunities to study HLB through genomic DNA sequence analyses (metagenomics). In this study, HLB-related bacteria in Asian citrus psyllid and citrus (represented by leaf midrib tissues) samples from southern California were analyzed. A metagenomic pipeline was developed to serve as a prototype for future bacteriomic research. This pipeline included steps of next-generation sequencing in Illumina platform, de novo assembly of Illumina reads, sequence classification using the Kaiju tool, acquisition of bacterial draft genome sequences, and taxonomic validation and diversity evaluation using average nucleotide identity. The identified bacteria in Asian citrus psyllids and citrus together included Bradyrhizobium, Buchnera, Burkholderia, “Candidatus Profftella armature,” “Candidatus Carsonella ruddii,” CLas, Mesorhizobium, Paraburkholderia, Pseudomonas, and Wolbachia. The whole genome of a CLas strain recently found in San Bernardino County was sequenced and classified into prophage typing group 1 (PTG-1), one of the five known CLas groups in California. Based on sequence similarity, Bradyrhizobium and Mesorhizobium were identified as possible source that could interfere with CLas detection using the 16S rRNA gene-based PCR commonly used for HLB diagnosis, particularly at low or zero CLas titer situation.

Summary Large amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high‐quality Ca . Tianyabacteria genomes representing two Ca . Tianyabacteria lineages (L1 and L2) in sediments 0–21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0–9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12–21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo‐inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca . Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.

Summary Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium‐ to high‐quality archaeal metagenome‐assembled genomes (MAGs) from the filamentous fragments of black‐odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca . Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo . Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood–Ljungdahl CO 2 ‐fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur‐, hydrogen‐, and arsenic‐transformation potentials. Comparative genomics indicated that the H 4 F Wood–Ljungdahl pathway of both Ca . Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca . Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.

Streptomycin (STR) has been used to control citrus huanglongbing (HLB) caused by ‘Candidatus Liberibacter asiaticus’ (CLas) via foliar spray. Here, we studied the residue dynamics of STR and its effect on CLas titers in planta applied by foliar spray and trunk injection of 3-year-old citrus trees that were naturally infected by CLas in the field. After foliar spray, STR levels in leaves peaked at 2 to 7 days postapplication (dpa) and gradually declined thereafter. The STR spray did not significantly affect CLas titers in leaves of treated plants as determined by quantitative PCR. After trunk injection, peak levels of STR were observed 7 to 14 dpa in the leaf and root tissues, and near-peak levels were sustained for another 14 days before significantly declining. At 12 months after injection, moderate to low or undetectable levels of STR were observed in the leaf, root, and fruit, depending on the doses of STR injected, with a residue level of 0.28 µg/g in harvested fruit at the highest injection concentration of 2.0 µg/tree. CLas titers in leaves were significantly reduced by trunk injection of STR at 1.0 or 2.0 g/tree, starting from 7 dpa and throughout the experimental period. The reduction of CLas titers was positively correlated with STR residue levels in leaves. The in planta minimum effective concentration of STR needed to suppress the CLas titer to an undetectable level (cycle threshold ≥36.0) was 1.92 µg/g fresh weight. Determination of the in planta minimum effective concentration of STR against CLas and its spatiotemporal residue levels in planta provides the guidance to use STR for HLB management.