Publications

4926

Although there are no known sources of genetic resistance, some Citrus spp. are reportedly tolerant to huanglongbing (HLB), presumably caused by ‘Candidatus Liberibacter asiaticus’. Time-course transcriptional analysis of tolerant rough lemon (Citrus jambhiri) and susceptible sweet orange (C. sinensis) in response to ‘Ca. L. asiaticus’ infection showed more genes differentially expressed in HLB-affected rough lemon than sweet orange at early stages but substantially fewer at late time points, possibly a critical factor underlying differences in sensitivity to ‘Ca. L. asiaticus’. Pathway analysis revealed that stress responses were distinctively modulated in rough lemon and sweet orange. Although microscopic changes (e.g., callose deposition in sieve elements and phloem cell collapse) were found in both infected species, remarkably, phloem transport activity in midribs of source leaves in rough lemon was much less affected by HLB than in sweet orange. The difference in phloem cell transport activities is also implicated in the differential sensitivity to HLB between the two species. The results potentially lead to identification of key genes and the genetic mechanism in rough lemon to restrain disease development and maintain (or recover) phloem transport activity. These potential candidate genes may be used for improving citrus tolerance (or even resistance) to HLB by genetic engineering.

ABSTRACT SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world’s oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade’s origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade. IMPORTANCE The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.

Summary Microautoradiography combined with fluorescence in situ hybridization (MAR‐FISH) was used to screen for potential polyphosphate‐accumulating organisms (PAOs) in full‐scale enhanced biological phosphorus removal (EBPR) plants. Clone library analyses and application of MAR‐FISH using newly designed probes revealed that small rods related to uncultured Halomonas within the gammaproteobacterial family Halomonadaceae were actively involved in uptake of orthophosphate. Although deeply branched in the Gammaproteobacteria , they were not targeted by the gammaproteobacterial probe (GAM42a). A part of them were also not targeted with the general bacterial probes (EUBmix). They could take up short‐chain fatty acids (e.g. acetate and propionate) and ethanol under both anaerobic and aerobic conditions. Polyhydroxyalkanoate storage was observed under anaerobic conditions. There was no indication of a denitrifying capability. A survey of the occurrence of these Halomonas ‐PAOs in 23 full‐scale EBPR plants revealed that they made up 0.5–5.7% of all bacteria in the plants, and were often in higher abundance than the well‐described PAOs ‘ Candidatus Accumulibacter phosphatis’. This indicates a potentially important role for these uncultured Halomonas bacteria in the EBPR process in full‐scale plants and we propose to name them ‘ Candidatus Halomonas phosphatis’.

Abstract An uncultured member of the phylum Chlorobi, provisionally named ‘Candidatus Thermochlorobacter aerophilum’, occurs in the microbial mats of alkaline siliceous hot springs at the Yellowstone National Park. ‘Ca. T. aerophilum’ was investigated through metagenomic and metatranscriptomic approaches. ‘Ca. T. aerophilum’ is a member of a novel, family-level lineage of Chlorobi, a chlorophototroph that synthesizes type-1 reaction centers and chlorosomes similar to cultivated relatives among the green sulfur bacteria, but is otherwise very different physiologically. ‘Ca. T. aerophilum’ is proposed to be an aerobic photoheterotroph that cannot oxidize sulfur compounds, cannot fix N2, and does not fix CO2 autotrophically. Metagenomic analyses suggest that ‘Ca. T. aerophilum’ depends on other mat organisms for fixed carbon and nitrogen, several amino acids, and other important nutrients. The failure to detect bchU suggests that ‘Ca. T. aerophilum’ synthesizes bacteriochlorophyll (BChl) d, and thus it occupies a different ecological niche than other chlorosome-containing chlorophototrophs in the mat. Transcription profiling throughout a diel cycle revealed distinctive gene expression patterns. Although ‘Ca. T. aerophilum’ probably photoassimilates organic carbon sources and synthesizes most of its cell materials during the day, it mainly transcribes genes for BChl synthesis during late afternoon and early morning, and it synthesizes and assembles its photosynthetic apparatus during the night.

A marine, magnetotactic bacterium, designated strain MMS-1T, was isolated from mud and water from a salt marsh in Woods Hole, Massachusetts, USA, after enrichment in defined oxygen-concentration/redox-gradient medium. Strain MMS-1T is an obligate microaerophile capable of chemoorganoheterotrophic and chemolithoautotrophic growth. Optimal growth occurred at pH 7.0 and 24–26 °C. Chemolithoautotrophic growth occurred with thiosulfate as the electron donor and autotrophic carbon fixation was via the Calvin–Benson–Bassham cycle. The G+C content of the DNA of strain MMS-1T was 47.2 mol%. Cells were Gram-negative and morphologically variable, with shapes that ranged from that of a lima bean to fully helical. Cells were motile by means of a single flagellum at each end of the cell (amphitrichous). Regardless of whether grown in liquid or semi-solid cultures, strain MMS-1T displayed only polar magnetotaxis and possessed a single chain of magnetosomes containing elongated octahedral crystals of magnetite, positioned along the long axis of the cell. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MMS-1T belongs to the family Rhodospirillaceae within the Alphaproteobacteria , and is distantly related to species of the genus Magnetospirillum . Strain MMS-1T is therefore considered to represent a novel species of a new genus, for which the name Magnetospira thiophila gen. nov., sp. nov. is proposed. The type strain of Magnetospira thiophila is MMS-1T ( = ATCC BAA-1438T = JCM 17960T).