Epiphyll deterrence to the leafcutter ant Atta cephalotes

Summary Epiphyll growth on leaves of the grapefruit Citrus paradisi and the understory cyclanth Cyclanthus bipartitus repelled the fungus-growing, leafcutter ant Atta cephalotes from harvesting leaves of these tropical plants. Experimental removal of epiphylls from leaves resulted in 2–3 times more herbivore damage by leafcutter ants as compared to matched leaves with epiphylls. Because of the protection from herbivore damage, host plants may derive a partial fitness benefit from association with epiphylls.     

Traffic dynamics of the leaf-cutting ant, Atta cephalotes

Colonies of Atta cephalotes (Myrmicinae: Formicidae) construct cleared paths between their nest and the vegetation sources at which they harvest leaf tissue. Here, we employ ideas from traffic engineering to study streams of laden and unladen ants on these paths. The relationship between average traffic speed and the concentration of workers on the road surface follows a relationship similar to what is expected by analogy to fluid dynamics. Although the traffic is composed of eusocial organisms with a common interest in group success, the coarse-grained behavior of Atta traffic displays little more coordination than a moving fluid. The relationship between speed and concentration implies that maximum flow rates (which are likely to be closely tied to colony-level rates of resource acquisition) occur at a relatively high concentration that keeps individual speeds well below their "free flow" maximum. We predict that this optimal concentration will characterize peak traffic throughout a trail network, and we propose a simple behavioral mechanism that would allow trails to be cleared to the correct width to provide the optimal concentration. Collisions (including encounters for antennation) are common in leaf-cutting ant traffic because traffic is not segregated into unidirectional streams. Nonetheless, we find a counterintuitive suggestion that flow rates (with concentration differences statistically removed) are higher when traffic is near a 50:50 mix of outbound and returning ants than when it contains majority flows in a single direction. Mixed-direction traffic may help disperse laden ants with reduced agility, thereby preventing inhomogeneities in the traffic stream that could clog the trail.     

Load-size determination in the leaf-cutting ant, Atta cephalotes

I examined load-size determination by a highly polymorphic leaf-cuttingant, Atta cephalotes, cutting leaves of artificial trees (branchesplaced in the top of plastic tubes). I compared load size forants cutting thin leaves (starfruit, Averrhoa carambola) andthick leaves (grapefruit, Citrus parodist). At each source,larger ants cut larger fragments. Distance from the nest hadno effect on load size. The mass of fragments cut by an antof a given size was significantly greater when cutting grapefruitleaves. The leaf area cut, however, showed no significant differencebetween the two leaf types. Leaf area increased approximatelyin proportion to ant body mass to the 0.6 power. As a resultof their method of load-size determination, ants of a givensize cut heavier loads when cutting the thicker leaves. Thisdifference, however, was counteracted at the colony level byrecruitment of larger ants, which cut smaller area fragmentsrelative to their body mass, to cut at thicker leaf sources.     

In vitro evaluation of Trichoderma and Gliocladium antagonism against the symbiotic fungus of the leaf-cutting ant Atta cephalotes

The antagonistic activity of Trichoderma and Gliocladium isolates against Attamyces sp., a symbiotic fungus of the leaf-cutting ant Atta cephalotes, was investigated. A. cephalotes cultures this fungus as the primary food source. Most of the Trichodema and Gliocladium isolates tested in vitro (82.6%) inhibited the Attamyces sp. mycelial growth, which was probably due to their colonization ability and competition for nutrients, both of them known mechanisms of some species of these genera. T. lignorum strain T-26 was the strongest inhibitor achieving a colonization of 23%. Microscopical observations indicate that the inhibitory effect was caused by an interaction that took place in close contact with the host hypha, causing wall deformation that led to the collapse of the turgor pressure. This revised version was published online in June 2006 with corrections to the Cover Date.     

Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant neotropical herbivores cultivate symbiotic fungus gardens on large quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers. Using metagenomic and metaproteomic techniques, we characterize the bacterial diversity and physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter and Escherichia. We show that these bacterial communities possess genes associated with lignocellulose degradation and diverse biosynthetic pathways, suggesting that they play a role in nutrient cycling by converting the nitrogen-poor forage of the ants into B-vitamins, amino acids and other cellular components. Our metaproteomic analysis confirms that bacterial glycosyl hydrolases and proteins with putative biosynthetic functions are produced in both field-collected and laboratory-reared colonies. These results are consistent with the hypothesis that fungus gardens are specialized fungus–bacteria communities that convert plant material into energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities in the ecology and evolution of herbivorous metazoans.     

Ontogenetic changes in forager polymorphism and foraging ecology in the leaf-cutting ant Atta cephalotes

In the leaf-cutting ant Atta cephalotes (L.) small colonies produce a relatively narrow size-range of small workers, whereas large colonies produce a much wider size-range of workers. In this study, I compared the foraging of four small A. cephalotes colonies (fewer than 5000 workers) with published data on foraging of large colonies to examine how colony size and worker size-range may be related to foraging ecology in leaf-cutting ants. I found that the foraging ecology of small A. cephalotes colonies is very different from that of large colonies. In small colonies, a relatively narrow size-range of foragers (1.4–6.7 mg, mean 3.3 mg) cut primarily herbs (ferns, grasses, and other small herbaceous plants) located within 7 m of the nest. In contrast, in large colonies, a broader size-range of workers (1.4–30 mg, mean 7.3 mg) participate in foraging, generally harvesting from trees 20–80 m from the nest, with larger workers cutting on trees with thicker and tougher leaves. Small colonies' dependence on small herbaceous plants near the nest may have a profound impact on distribution of A. cephalotes. A. cephalotes colonies are rarely found in primary forest, where the low occurrence of small herbaceous plants in the understory may preclude the establishment of young colonies.     

Forager polymorphism, size-matching, and load delivery in the leaf-cutting ant, Atta cephalotes

Abstract.

• 1 This study examined the importance of forager polymorphism and division of labour among foragers of different size for the economics of load delivery in a leaf-cutting ant, Atta cephalotes (L.). I collected A.cephalotes foragers coming down trees carrying leaf fragments to evaluate the degree of match between forager mass and the density (mass per unit area) of leaves being cut, and to quantify how this match affects whether the mass of leaf fragments cut by the ants are within the range which maximizes the rate and efficiency of load delivery.
• 2 Foragers ranged 23-fold in mass (1.4–32.1 mg). On average, larger workers cut at denser leaf sources. Leaf fragment area increased with ant mass, but relative area (fragment area/ant mass) decreased with ant mass. The density of a leaf type had little or no effect on the area cut by ants of a given size. As a result, ants of a given mass cut heavier fragments from the denser leaves. The effect of leaf density, however, was partly counteracted at the colony level by recruitment of larger ants, which cut smaller area fragments relative to their body mass, to cut at denser leaf sources.
• 3 Despite a fairly high variance in the relationship between ant mass and fragment mass, overall 87% of the laden ants (74–100% for different trees) carried leaf fragments in the 1.5–6 times body mass range. Earlier studies indicate that loads in this range yield the highest biomass transport rate and transport efficiency. Thus, the variance falls within bounds such that it has little effect on load transport efficiency. Having a broad range in optimal load mass may be considered an adaptation to the expected variability in load masses.
• 4 If there were no correlation between ant mass and leaf density, mismatches between ant mass and load mass would be more common than observed. Thus, size-matching of larger workers to cut denser leaves increases the rate and ergonomic efficiency of load delivery.

     

Some factors affecting the site and pattern of leaf-cutting activity in the ant Atta cephalotes L.

An account is given of some aspects of the leaf-cutting behaviour of the ant Atta cephalotes L. Chemical and physical factors that determine the site of cutting are described, and the significance of these in the pattern of plant attack is discussed.     

The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing

Corynebacterium urealyticum is a lipid-requiring, urealytic bacterium of the human skin flora that has been recognized as causative agent of urinary tract infections. We report the analysis of the complete genome sequence of C. urealyticum DSM7109, which was initially recovered from a patient with alkaline-encrusted cystitis. The genome sequence was determined by a combination of pyrosequencing and Sanger technology. The chromosome of C. urealyticum DSM7109 has a size of 2,369,219bp and contains 2024 predicted coding sequences, of which 78% were considered as orthologous with genes in the Corynebacterium jeikeium K411 genome. Metabolic analysis of the lipid-requiring phenotype revealed the absence of a fatty acid synthase gene and the presence of a beta-oxidation pathway along with a large repertoire of auxillary genes for the degradation of exogenous fatty acids. A urease locus with the gene order ureABCEFGD may play a pivotal role in virulence of C. urealyticum by the alkalinization of human urine and the formation of struvite stones. Multidrug resistance of C. urealyticum DSM7109 is mediated by transposable elements, conferring resistances to macrolides, lincosamides, ketolides, aminoglycosides, chloramphenicol, and tetracycline. The complete genome sequence of C. urealyticum revealed a detailed picture of the lifestyle of this opportunistic human pathogen.     

A human genome structural variation sequencing resource reveals insights into mutational mechanisms

Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation. We develop a resource based on capillary end sequencing of 13.8 million fosmid clones from 17 human genomes and characterize the complete sequence of 1054 large structural variants corresponding to 589 deletions, 384 insertions, and 81 inversions. We analyze the 2081 breakpoint junctions and infer potential mechanism of origin. Three mechanisms account for the bulk of germline structural variation: microhomology-mediated processes involving short (2-20 bp) stretches of sequence (28%), nonallelic homologous recombination (22%), and L1 retrotransposition (19%). The high quality and long-range continuity of the sequence reveals more complex mutational mechanisms, including repeat-mediated inversions and gene conversion, that are most often missed by other methods, such as comparative genomic hybridization, single nucleotide polymorphism microarrays, and next-generation sequencing.     

Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+) kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems.     

Complete genome sequence of the halophilic PHA-producing bacterium Halomonas sp. SF2003: insights into its biotechnological potential

World Journal of Microbiology and Biotechnology - The present study investigated biodegradation and removal of Reactive Red 198 (RR198) dye from aqueous environments using a new bacterial...     

A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle

We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ~35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity.     

The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese

Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.     

Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea

Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.     

The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages

One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.