The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability

Chromobacterium violaceum is one of millions of species of free-living microorganisms that populate the soil and water in the extant areas of tropical biodiversity around the world. Its complete genome sequence reveals (i) extensive alternative pathways for energy generation, (ii) ≈500 ORFs for transport-related proteins, (iii) complex and extensive systems for stress adaptation and motility, and (iv) wide-spread utilization of quorum sensing for control of inducible systems, all of which underpin the versatility and adaptability of the organism. The genome also contains extensive but incomplete arrays of ORFs coding for proteins associated with mammalian pathogenicity, possibly involved in the occasional but often fatal cases of human C. violaceum infection. There is, in addition, a series of previously unknown but important enzymes and secondary metabolites including paraquat-inducible proteins, drug and heavy-metal-resistance proteins, multiple chitinases, and proteins for the detoxification of xenobiotics that may have biotechnological applications

Glyptothrips silvaticus

<i>Glyptothrips silvaticus</i> (Hood, 1957b) <p>(Figs 61–65)</p> <p> This is a paler species than most <i>Glyptothrips</i>, with a greyish yellow or light brown colour (Fig. 61), contrasting to the dark brown or golden yellow shades more commonly seen in the genus. The sternal pore plate of males is a narrow transverse band, a trait more commonly seen in North American <i>Glyptothrips</i> species. The only other Brazilian species with this type of pore plate is <i>G. subcalvus</i>, a much darker species with several morphological differences to <i>G. silvaticus</i> (Table 2). It also bears thickened and capitate setae on all femora (Fig. 63) like <i>G. fuscipes</i>, but they are not as straight and elongate as in that mostly dark brown species.</p> <p>Known wing forms: micropterous.</p> <p> <b>Specimens studied</b>. Lectotype ♀; Brazil, Santa Catarina, Nova Teutônia, under fallen leaves, vi.1954 (F. Plaumann), at NMNH.</p>Published as part of <i>Lindner, Mariana Flores, Ferrari, Augusto, Lima, Élison Fabrício Bezerra & Cavalleri, Adriano, 2023, Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae), pp. 31-57 in Zootaxa 5375 (1)</i> on page 51, DOI: 10.11646/zootaxa.5375.1.2, <a href="http://zenodo.org/record/10170724">http://zenodo.org/record/10170724</a&gt

FIGURE 4 in Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae)

FIGURE 4. Thysanoptera chaetotaxy. Only setae mentioned in this work are indicated.Published as part of <i>Lindner, Mariana Flores, Ferrari, Augusto, Lima, Élison Fabrício Bezerra & Cavalleri, Adriano, 2023, Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae), pp. 31-57 in Zootaxa 5375 (1)</i> on page 35, DOI: 10.11646/zootaxa.5375.1.2, <a href="http://zenodo.org/record/10170724">http://zenodo.org/record/10170724</a&gt

Glyptothrips flavescens Hood 1912

<i>Glyptothrips flavescens</i> Hood, 1912 <p>(Figs 25–27)</p> <p> This, the type species of <i>Glyptothrips</i>, has several unique traits. Besides the 7-segmented antennae, it lacks thick and capitate ventrolateral setae, has the AA setae closer to the reduced AM (only seen elsewhere in <i>G. floridensis</i> and <i>G. interior</i>), and the sculpture on thorax and abdomen bears multiple tubercles (Fig. 26).</p> <p>Known wing forms: macropterous, micropterous and apterous.</p> <p> <b>Specimens studied</b>. Holotype ♀; United States of America, Illinois, Grand Tower, in sweepings from grass, 10.vii.1909 (C.A. Hart), at NMNH.</p> <p>Paratype one ♀, United States of America, Illinois, Putaski, in sweeping from grass, 28.vi.1909 (Cleared in KOH, remounted 1952), at NMNH.</p> <p>One ♀ (non-type); Brazil, Rio Grande do Sul, São Francisco de Assis, 4.ii.2013 (A. Cavalleri), at UFRGS.</p>Published as part of <i>Lindner, Mariana Flores, Ferrari, Augusto, Lima, Élison Fabrício Bezerra & Cavalleri, Adriano, 2023, Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae), pp. 31-57 in Zootaxa 5375 (1)</i> on page 45, DOI: 10.11646/zootaxa.5375.1.2, <a href="http://zenodo.org/record/10170724">http://zenodo.org/record/10170724</a&gt

Glyptothrips Hood

<i>Glyptothrips</i> Hood <p> <i>Glyptothrips</i> Hood, 1912: 116. Type species <i>Glyptothrips flavescens</i> Hood, 1912, by monotypy.</p> <p> There is no unique character state to diagnose this genus, but the following combination of character states seem useful to distinguish a member of the genus from other Glyptothripini: (1) body strongly reticulate (Figs 6, 15, 58), except the tube which has at most some weak sculpture basally (Figs 16, 45, 59); (2) pronotal AM reduced (Figs 20, 32, 69); (3) pterothoracic ventrolateral setae usually thick and capitate (Figs 21, 33, 62), except in <i>G. arkansanus</i>, <i>G. bucca</i>, <i>G. flavescens</i> and <i>G. reticulatus</i>. In addition, all observed <i>Glyptothrips</i> species share the following: head incut behind globose/moruloid eyes (Figs 26, 48); PO setae and all pronotal setae except AM well-developed with dilated tips (Figs 15, 32); antennal segments II–IV with at least one pair of capitate setae (except in <i>G. bucca</i>) (Fig. 35); prosternal basantra present; tube with straight, tapering sides (Figs 7, 11); fore tarsi armed with a tooth (except in <i>G. arkansanus</i>) (Figs 42, 48); fore wings without duplicated cilia.</p> <p> <i>Character state variation amongst included species</i>:</p> <p> <i>Colouration</i>: Body structures vary in colour, which is heavily influenced by how the specimen was prepared for slide mounting: many species were described from individuals not macerated in NaOH prior to mounting. Several type specimens were also mounted initially in Hoyers, a mounting media not as durable as Canada Balsam, and much colour information could be modified or lost (e.g. Figs 28–30). Some patterns remain useful for identifications. Original descriptions state some species are yellowish (e.g. <i>G. interior</i> — Fig. 41 and <i>G. silvaticus</i> — Fig. 61) or darker brown (e.g. <i>G. claviger</i> — Fig. 14 and <i>G. subcalvus —</i> Fig. 66). However, some macerated specimens identified structurally as <i>G. subcalvus</i> have a lighter, yellowish colour (e.g. Figs 69–72).</p> <p> Antennae are frequently of similar colour to the head, with distal antennal segments progressively darker, and darker antennal segments (especially IV–VI) often have the basal areas and/or pedicels lighter (Figs 25, 35, 43). In <i>G. arkansanus</i> the antennae are mostly yellow with only the last antennal segment slightly darker (Fig. 5); and <i>G. subcalvus</i> has the first two antennal segments very pale yellow, much lighter than the head (Figs 66, 68).</p> <p> Head and thorax are commonly the same colour (Figs 9, 41), or the thorax is partially or fully darker than the head (Figs 47, 57). The abdomen is frequently paler or gets progressively paler distally (Fig. 31). Some species have a darker antecostal ridge and/or spot on tergites II–VII (<i>G. divergens</i> — Fig. 19; <i>G. interior</i> — Fig. 41; <i>G. saltuarius</i> — Fig. 57; <i>G. silvaticus —</i> Fig. 61). Some species have two longitudinal pale lines dividing the tergites into thirds (<i>G. arkansanus</i> — Figs 5–7), and the posteromedian area of the tergite may be much paler. Similar lines are present but not as obvious in <i>G. flavescens</i> (Fig. 26), and in <i>G. subcalvus</i> the tergal median third seems to be darker than the rest of the abdomen (Fig. 66). The tube is also variable between species, but more commonly a similar (Figs 7, 27) or darker colour to the previous abdominal segments (Figs 22, 65). The basal and/or apical areas of the tube are frequently lighter or darker than the middle of the tube (Figs 45, 73).</p> <p> <i>Head</i>: all <i>Glyptothrips</i> species have the head fully covered by strong reticulation, both on dorsal and ventral surfaces (Figs 6, 20, 67). The genae vary from almost straight (<i>G. divergens</i> — Fig. 20; <i>G. hylaeus —</i> Fig. 38), to strongly curved (<i>G. bucca</i> — Fig. 10; <i>G. subcalvus —</i> Fig. 67). Observed head length x greatest width ratio from original descriptions vary from 1 (<i>G. floridensis</i>) to 1.5 (<i>G. longiceps</i>). However, this character should be used with caution; it can be affected by slide mounting, and ranges can overlap between species (Table 2).</p> <p> <i>...Continued on the next page</i></p> <p>¹All given ratios and measures were obtained from original descriptions and/or the individuals listed in the “observed specimens” section under each species in the manuscript. Intraspecific variation has not been studied for the majority of the species due to the limited number of individuals available.</p> <p> Most species in the genus have small and acute postocellar, occipital and head lateral setae, but <i>G. floridensis</i> is illustrated by Stannard (1955) with the occipital and many lateral setae as long and capitate as the PO. The occipital setae have dilated tips also in <i>G. claviger</i> (Fig. 15) and <i>G. interior</i> (Fig. 42), but neither of these species has the head lateral setae thickened or capitate. Length of PO varies from very short and inconspicuous (<i>G. divergens</i> — Fig. 20), to as long or longer than the compound eye (<i>G. silvaticus</i> — Fig. 63) (Table 2).</p> <p> <i>Antennae</i>: the type species, <i>G. flavescens</i>, has only 7 antennal segments with antennal segments VII and VIII fused (Fig. 26). <i>G. arkansanus</i> approximates this condition in the genus, with antennal segments VII–VIII broadly joined but separated by a suture. All other <i>Glyptothrips</i> species have VII and VIII clearly separated (Figs 12, 23, 35). The most common sense cone formula in <i>Glyptothrips</i> is 3 sense cones on antennal segment III and 4 on IV. However, reductions in the number of sense cones are known in <i>G. bucca</i>, <i>G. flavescens</i>, <i>G. interior</i>, <i>G. reticulatus</i> and <i>G. subcalvus</i> (Table 2).</p> <p> The shape of antennal segments is also variable within the genus, from very short and globose in <i>G. flavescens</i> (Fig. 26) and <i>G. arkansanus</i> (Fig. 5), to elongate in <i>G. divergens</i> (Fig. 23) and <i>G. fuscipes</i> (Fig. 35). Some species are also intermediate between these extremes, such as <i>G. bucca</i>, <i>G. subcalvus</i> (short but not globose antennal segments), <i>G. hylaeus</i> or <i>G. silvaticus</i>.</p> <p> <i>Prothorax</i>: most species have the pronotum reticulate (Figs 6, 20), but the sculpture can be less obvious in some species (Fig. 69). The epimeral sutures are usually incomplete. The position of AA setae is at or very close to the pronotum anterior angles in most <i>Glyptothrips</i> species, but in at least <i>G. flavescens</i> (Fig. 26) and <i>G. floridensis</i> this pair of setae arises close to AM.</p> <p> <i>Pterothorax</i>: meso- and metanotum are both clearly sculptured, usually with equiangular reticles without any internal markings (Figs 6, 21). However, at least <i>G. flavescens</i> and some specimens of <i>G. claviger</i> have “tubercles” in the metanotum, in place of some of the sculpture lines (Fig. 26). The ventrolateral setae are thick and capitate in most <i>Glyptothrips</i> (Figs 21, 62), with the only exceptions listed in the proposed diagnosis above.</p> <p> <i>Legs</i>: all legs usually have similar sizes and sculpturing, and are covered in many acute setae (Figs 5–6, 14–15). The fore tibia does not have tubercles. In <i>G. fuscipes</i>, all femora and the fore tibiae have at least one or two elongate, thick and capitate setae (Figs 31, 33); most other <i>Glyptothrips</i> species lack such setae, although a short but capitate seta has been seen in the fore femora of some specimens of <i>G. claviger</i>, <i>G. longiceps</i>, <i>G. reticulatus</i>, <i>G. silvaticus</i> (Fig. 63) and <i>G. subcalvus</i>.</p> <p> <i>Wings</i>: there are multiple wing forms within the genus, with macropterous (Fig. 5), micropterous (Fig. 15) and apterous (Fig. 55) specimens known. Five species (<i>G. arkansanus</i>, <i>G. flavescens</i>, <i>G. reticulatus</i>, <i>G. saltuarius</i> and <i>G. subcalvus</i>) are known to have two or more wing morphs. The degree of wing development is frequently associated to changes in some character states, especially when comparing macropterae (eyes sometimes larger, ocelli present, pelta not as wide) with apterae (eyes sometimes reduced, ocelli reduced or absent, pelta wide and rectangular or oval in shape) (Mound 1977, 2005; Mound & Marullo 1996; personal observations).</p> <p> <i>Abdomen</i>: the pelta is highly variable, and at least partially associated with the degree of wing development. The most common shape seems to be a broad oval or rectangular plate (Figs 10, 26, 44, 69), however some species may have a triangular, trapezoidal (Figs 15, 36) or hat-shaped (Fig. 6) pelta. Tergites II–IX are sculptured, with the median posterior area weaker or sometimes smooth (Figs 6, 44, 58). The three main setal pairs on tergite IX are well developed, with S2 reduced in males (Fig. 45). Setae S1 are most frequently dilated or capitate (Figs 45, 73), while S2 are more frequently acute or blunt (Table 2). The tube is mostly smooth, with weak lines of sculpture basally (Figs 7, 16, 39), but never with strong reticulation as in <i>Chamaeothrips</i> Hood or <i>Eschatothrips</i> species. The tube is usually shorter than the head or almost as long as the head; only two species (<i>G. divergens</i> and <i>G. flavescens</i>) have recorded specimens where the tube is slightly longer than the head (Figs 19, 25).</p>Published as part of <i>Lindner, Mariana Flores, Ferrari, Augusto, Lima, Élison Fabrício Bezerra & Cavalleri, Adriano, 2023, Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae), pp. 31-57 in Zootaxa 5375 (1)</i> on pages 34-38, DOI: 10.11646/zootaxa.5375.1.2, <a href="http://zenodo.org/record/10170724">http://zenodo.org/record/10170724</a&gt

Glyptothrips fuscipes

<i>Glyptothrips fuscipes</i> (Hood, 1954) <p>(Figs 31–36)</p> <p> This species can be differentiated from most other <i>Glyptothrips</i> species by its brown colouration (including legs, which in other species are usually yellow or at least lighter than the body; Figs 31, 33), and presence of rather thick and elongate capitate setae on all femora and fore tibiae (Fig. 31). Other species in the genus may present this type of thickened setae at least on fore femora (e.g. <i>G. claviger</i>, <i>G. silvaticus</i>), but they are not as elongate and numerous as in <i>G. fuscipes</i>.</p> <p>Known wing forms: micropterous.</p> <p> <b>Specimens studied</b>. Holotype ♀; Brazil, Santa Catarina, Nova Teutônia, viii.1952 (F. Plaumann), at NMNH.</p> <p>Paratypes one ♂ and one ♀, same collection data and depositary as holotype.</p>Published as part of <i>Lindner, Mariana Flores, Ferrari, Augusto, Lima, Élison Fabrício Bezerra & Cavalleri, Adriano, 2023, Morphological identification of Glyptothrips species (Thysanoptera: Phlaeothripidae), pp. 31-57 in Zootaxa 5375 (1)</i> on page 46, DOI: 10.11646/zootaxa.5375.1.2, <a href="http://zenodo.org/record/10170724">http://zenodo.org/record/10170724</a&gt