The microtubule analog protein, FtsZ, in the endosymbiont of trypanosomatid protozoa

Blastocrithidia culicis and Crithidia deanei are trypanosomatids that harbor an endosymbiotic bacterium in their cytoplasm. In prokaryotes, numerous proteins are essential for cell division, such as FtsZ, which is encoded by filament-forming temperature-sensitive (fts) genes. FtsZ is the prokaryotic homolog of eukaryotic tubulin and is present in bacteria and archaea, and has also been identified in mitochondria and chloroplasts. FtsZ plays a key role in the initiation of cytokinesis. It self-assembles into the Z ring, which establishes the division plane during septation. In this study, immunoblotting analysis using a FtsZ polyclonal antibody, revealed a 40-kDa band characteristic of FtsZ in endosymbiont fractions and in whole trypanosomatid homogenates, but not in whole cell extracts of aposymbiotic strains. Confocal microscopy and ultrastructural analysis revealed a specific and dispersed labeling over the endosymbiont. Bars and ring-like structures, which are suggestive of the presence of Z-rings, were never observed, even during the division of the symbiont. This peculiar distribution of FtsZ may represent an arrangement of cytoskeleton protein intermediate between prokaryotic and eukaryotic cells. The endosymbiont ftsz gene was completely sequenced after amplification of DNA from symbiont-bearing trypanosomatids or from pure endosymbiont fractions, using PCR and specific primers. The sequences obtained from the endosymbionts from C. deanei and B. culicis were very similar, and were most closely related to bacteria from the genus Pseudomonas.     

Origin and evolution of the light-dependent protochlorophyllide oxidoreductase (LPOR) genes

Abstract: Light‐dependent NADPH‐protochlorophyllide oxidoreductase (LPOR) is a nuclear‐encoded chloroplast protein in green algae and higher plants which catalyzes the light‐dependent reduction of protochlorophyllide to chlorophyllide. Light‐dependent chlorophyll biosynthesis occurs in all oxygenic photosynthetic organisms. With the exception of angiosperms, this pathway coexists with a separate light‐independent chlorophyll biosynthetic pathway, which is catalyzed by light‐independent protochlorophyllide reductase (DPOR) in the dark. In contrast, the light‐dependent function of chlorophyll biosynthesis is absent from anoxygenic photosynthetic bacteria. Consequently, the question is whether cyanobacteria are the ancestors of all organisms that conduct light‐dependent chlorophyll biosynthesis. If so, how did photosynthetic eukaryotes acquire the homologous genes of LPOR in their nuclear genomes? The large number of complete genome sequences now available allow us to detect the evolutionary history of LPOR genes by conducting a genome‐wide sequence comparison and phylogenetic analysis. Here, we show the results of a detailed phylogenetic analysis of LPOR and other functionally related enzymes in the short chain dehydrogenase/reductase (SDR) family. We propose that the LPOR gene originated in the cyanobacterial genome before the divergence of eukaryotic photosynthetic organisms. We postulated that the photosynthetic eukaryotes obtained their LPOR homologues through endosymbiotic gene transfer.     

Artificial induction of the apple replant problem byPenicillium claviforme inoculation

Inoculation of apple seedling roots withPenicillium claviforme reduced plant growth and resulted in morphological changes of roots resembling those found in seedlings growing in ‘apple replant problem’ soil (apple-sick soil). The introduced fungus persisted in the rhizosphere throughout the 30-month test period. The numbers of colony-forming units (CFU) ofPenicillium claviforme, as well as the ‘total’ number of CFU of micromycetes, were higher in the rhizoplane of the inoculated seedling in comparison with uninoculated plants. The numbers of CFU of phytotoxic micromycetes in the rhizosphere soil of inoculated seedlings were also proportionally higher. Apple tree growth was also reduced when seedlings were inoculated with the flucrescent bacteriumPseudomonas putida; however, no morphological changes were observed in the roots. Both micro-organisms introduced into the apple seedling rhizosphere caused changes in the microbial community. Inoculation withPenicillium claviforme andPseudomonas putida caused a decrease in the number of mycolytic bacteria in the rhizoplane of apple seedlings.     

Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and,with the exception of endosymbiotic gene transfers,few ancient transfer events persist

While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.     

The tetrapyrrole synthesis pathway as a model of horizontal gene transfer in euglenoids

The history of euglenoids may have begun as early as ~2 bya. These early phagotrophs ate cyanobacteria, archaea, and eubacteria, and the subsequent appearance of red algae and chromalveolates provided euglenoids with additional food sources. Following the appearance of green algae, euglenoids acquired a chloroplast via a secondary endosymbiotic event with a green algal ancestor. This endosymbiosis also involved a massive transfer of nuclear‐encoded genes from the symbiont nucleus to the host. Expecting these genes to have a green algal origin, this research has shown, through the use of DNA‐sequences and the analysis of phylogenetic relationships, that many housekeeping genes have a red algal/chromalveolate ancestry. This suggested that many other endosymbiotic/horizontal gene transfers, which brought genes from chromalveolates to euglenoids, may have been taking place long before the acquisition of the chloroplast. The investigation of the origin of the enzymes involved in the tetrapyrrole synthesis pathway provided insights into horizontal gene transfer in euglenoids and demonstrated that the euglenoid nuclear genome is a mosaic comprised of genes from the ancestral lineage plus genes transferred endosymbiotically/horizontally from green, red, and chromalveolates lineages.     

Biodeterioration of ornamental marble statues in the Boboli Gardens (Florence, Italy)

The colonisation of ornamental marble statues in theBoboli Gardens of Florence (Italy) by photosyntheticmicro-organisms was investigated. The greenmicroalga Coccomyxa was the first colonizer ofnewly restored marble surfaces, appearing one yearafter the periodic cleaning and restoration of thestatues. Two years after restoration this alga gaverise to very thin green biofilms, with densitiesreaching about 3 × 10² cells cm^-2. Later,the biofilms were enriched by cyanobacterial forms,which became dominant. In about six years, aphotosynthetic microbial community, amounting to about3 × 10⁴ cells cm^-2, and structurally similarto that occurring on the unrestored statues wasdeveloped. This epilithic community showed amarked biodiversity; the main representative formsincluded Chroococcidiopsis, Leptolyngbya,Pleurocapsa, Coccomyxa and Apatococcus.Coccomyxa initiated the colonisation of themarble surfaces, favoured in this process by itsfacultative oligotrophic capacity and high cellsurface hydrophobicity, combined with tolerance ofhigh light intensity. The other investigated isolatedstrains did not show this set of features. Thesecretion of polysaccharidic substances and cellsurface hydrophobicity enhancing the capacity toadhere, favoured permanent colonisation of thecyanobacterial population. Indeed, the majority of thecyanobacterial strains (90%), were shown to besurrounded by exopolysaccharidic envelops, whichcontributed to the formation of stable microbialbiofilms, and possessed variable cell surfacehydrophobicity.     

Decomposition of duckweed (Lemna gibba) under axenic and microbial [-2pt] conditions: flux of nutrients between litter water and sediment, the impact of leaching and microbial degradation

The decomposition of axenic Lemna gibba has been studied over a 200 day period under laboratory conditions in the presence and absence of wastewater micro-organisms. The residual mass of plant litter in the decomposition vessels decreased three times more rapidly under biotic than abiotic conditions. The organic matter in the duckweed litter lost about half its weight within 67.9 days in the presence of micro-organisms while more than 200 days were required in axenic vessels. In the former case, AFDW loss followed an exponential pattern of decay. The rate constant was 0.0102 day ^–1 and the decay was virtually complete after 200 days. The C and K concentration of the remaining duckweed litter decreased; the N, Ca, Fe and B concentration increased in both treatments. The concentration of total N, P, K, Mg, and Mo increased in the receiving water in both treatments but was much higher under biotic than abiotic conditions. Mass balances of nutrients in the vessels and flux of these nutrients between compartments in the vessels (duckweed litter, water and sediment) have been determined. Under axenic conditions the release of elements was very slow. Only notably potassium leaching had occurred. Leaching of potassium, magnesium and organic carbon took place mainly during the first term of incubation and then slowed down. Under biotic decomposition the elemental content of the litter decreased by more than 50% over 43 days for K, 53 days for Mo, 64 days for C, 81 days for Mg, 101 days for S, 104 days for P, 108 days for Na, 111 days for N, 140 days for B. Calcium and iron immobilised in the litter. Most of the released N, S, P, K, Mg and Mo remained in the water, but B and Mn settled into the sediment. The result of the investigation demonstrated that the nutrient flux from decomposing duckweed litter is mainly a microbially mediated process.     

Though with constraints imposed by endosymbiosis,preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network

Chloroplasts evolved as a result of endosymbiosis, during which sophisticated mechanisms evolved to translocate nucleus‐encoded plastid‐targeted enzymes into the chloroplast to form the chloroplast metabolic network. Given the constraints and complexity of endosymbiosis, will preferential attachment still be a plausible mechanism for chloroplast metabolic network evolution? We answer this question by analysing the metabolic network properties of the chloroplast and a cyanobacterium, Synechococcus sp. WH8102 (syw). First, we found that enzymes related to more ancient pathways are more connected, and synthetases have the highest connectivity. Most of the enzymes shared by the two densest cores between the chloroplast and syw are synthetases. Second, the highly conserved functional modules mainly consist of highly connected enzymes. Finally, isozymes and enzymes from endosymbiotic gene transfer (EGT) were distributed mainly in conserved modules and showed higher connectivity than nonisozymes or non‐EGT enzymes. These results suggest that even with severe evolutionary constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network. However, the current analysis may not completely differentiate whether the chloroplast network properties reflect the evolution of the chloroplast network through preferential attachment or has been inherited from its cyanobacterial ancestor. To fully differentiate these two possibilities, further analyses of the metabolic network structure properties of organisms at various intermediate evolutionary stages between cyanobacteria and the chloroplast are needed.     

Ultra-violet radiation for the inactivation of microorganisms in hydroponics

Summary The growth of microorganisms in the nutrient solution of a circulating hydroponic system was suppressed by ultra-violet radiation. Applied for three hours daily (572 Jm⁻² h⁻¹) throughout experiments in which tomato and corn were grown, it was effective in reducing the population of microorganisms from between 500–800·10³ to 10–50·10³ cells per ml.