Beggiatoa

''Beggiatoa'' is a genus of '' Gammaproteobacteria'' belonging the order ''Thiotrichales,'' in the '' Pseudomonadota'' phylum. This genus was one of the first bacteria discovered by Ukrainian botanist Sergei Winogradsky. During his research in Anton de Bary's laboratory of botany in 1887, he found that ''Beggiatoa'' oxidized  hydrogen sulfide (H₂S) as energy source, forming intracellular  sulfur droplets, oxygen is the terminal electron acceptor and CO₂ is used as carbon source. Winogradsky named it in honor of the Italian doctor and botanist  Francesco Secondo Beggiato (1806 - 1883), from Venice. Winogradsky referred to this form of metabolism as "inorgoxidation" (oxidation of inorganic compounds), today called chemolithotrophy. These organisms live in sulfur-rich environments such as soil, both marine and freshwater, in the deep sea hydrothermal vents and in polluted marine environments. The finding represented the first discovery of lithotrophy. Two species of Beggiatoa have been formally described: the type species ''Beggiatoa alba'' and ''Beggiatoa leptomitoformis'', the latter of which was only published in 2017. This colorless and filamentous bacterium, sometimes in association with other sulfur bacteria (for example the genus Thiothrix), can be arranged in biofilm visible to the naked eye formed by a very long white filamentous mat, the white color is due to the stored sulfur. Species of ''Beggiatoa'' have cells up to 200 µm in diameter and they are one of the largest prokaryotes on Earth.

Taxonomy

The genera ''Beggiatoa'' is a quiet diverse group as it has representatives occupying several habitats and niches, both in fresh and salt water. In the past they have been confused as close relatives of ''Oscillatoria'' spp. ('' Cyanobacteria'') for the morphology and motility characters, but 5S rRNA analysis showed that members of ''Beggiatoa'' are phylogenetically distant from ''Cyanobacteria'' being members of the '' Gammaproteobacteria'' phylum.

The capability to oxidize sulfide and store sulfur are the main features which separates ''Beggiatoa'' and closely related ''Thioploca'' as filamentous colorless sulfur bacteria from other filamentous bacteria (like cyanobacteria and the nonsulfur-oxidizing ''Cytophaga'' and ''Flexibacter'') Another defining feature is the ability to store nitrate inside the vacuoles of the wide marine species’ cells. 16S rRNA sequences base studies inferred that this characteristic is shared between members of a monophyletic clade nested in the ''Beggiatoa'' genera; this clade also includes members of ''Thioploca'' and ''Thiomargarita'', both presenting only slight differences with Beggiatoas: whereas the former grows sharing a common slime sheath, the latter has not conserved filamentous growth and forms chains of rounded cells. Since the phylogenic history do not reflect the nomenclature, there's a need for a new denomination of genera and species. The Neo-type strain is the B18LB and it settled the criteria for identification of the freshwater species ''Beggiatoa alba''.

According t
NCBI
database only two species of ''Beggiatoa'' spp. have been validly published: ''Beggiatoa alba'', and ''Beggiatoa leptomitoformis.''

Genetic

Because of the lack of pure culture, little is known about the genetic of ''Beggiatoa''. ''Beggiatoa alba'' show a GC content between 40 and 42.7 mol%, the presence of two or three similar plasmids and the genome size of ''Beggiatoa alba'' strain B18LD result to be about 3Megabase (Mb). An important study about the genomic of ''Beggiatoa'' analyzed the sequences obtained from two single filaments of a vacuolated strain. Optical mapping showed that the genome size was about 7.4Mb and the sequence analyses detected pathways for sulfur oxidation, nitrate and oxygen respiration, and CO₂ fixation, confirming the chemolithoautotrophic physiology of ''Beggiatoa''. Furthermore, comparative genomics indicates horizontal gene transfer between ''Beggiatoa'' and ''Cyanobacteria'' of storage, metabolic, and gliding abilities.

Morphology and motility

By the observation of their morphological characteristics, ''Beggiatoa'' spp. can be divided into three categories:

# Freshwater strains, characterized by narrow filaments with no vacuoles;
# Narrow marine strains, without vacuoles (filaments' diameter of about 4.4 µm);
# Larger marine strains, with vacuoles for nitrate storing (filaments' diameter vary between 5 to 140 µm)
Obviously, this classification is purely ideal so some exceptions can exist. Narrow filaments are usually composed by cylindrical cells which length is about 1.5 to 8 times their thickness; wider filaments instead are disk-shaped with cell lengths from 0.10 to 0.90 times their cell width. In all of the cultured strains the terminal cells of the filaments appear rounded. Although they are Gram-negative bacteria, ''Beggiatoa'' show unusual cell-wall and membrane organization. Sometimes are present further membranes that cover the peptidoglycan layer and the number of this addictional membranes is very variable. Their presence maybe is due to the harsh conditions in which some of these organisms live. Even the intracellular granules can be covered by extra-membranes structure. Beside the sulfur granules, the cells often show the presence of similarly stored granules of polyhydroxybutyrate and polyphosphate. Very common in large marine vacuolated ''Beggiatoa'' are hollow-structured filaments, composed by cells with a narrow cytoplasm surrounding a large central vacuole, exploited for nitrate storing.

The filaments move by gliding and this movement is likely connected to string-like structures in the outer membrane and trans- peptidoglycan channels. Sometimes the filaments can also break through the formation of necridia cell in the middle of the filament. The motility of the filament is very important for the adaptability of the bacteria, because it allows to move on more suitable conditions for the cellular metabolism. The main drivers that guide the movement of ''Beggiatoa'' filaments are high oxygen and sulfide levels and light exposure, from which the filaments move away.

Cell growth

''Beggiatoa'' reproducing strategy is fragmentation. The growth of a colony leading to mat development is obtained through alternating filament elongation and breakage. Breakage can happen essentially in the middle of a stretched filament, at the tip of a filament loop or where a tip of a loop was once placed. The presence of sacrificial cells is fundamental as they interrupt the communication between two parts of one filament; in this way each section can change its gliding direction causing the split.

The average filament length achieved through this process is also result of gene-environment interactions as, for instance, the growth and position of the filament is function of vertical gradients of oxygen and sulfide. Therefore, it is proposed that good environmental conditions will paradoxically cause cell death in order to enhance filament breakage, thus reproduction.

Metabolism

''Beggiatoa'' group is mainly composed by chemolithotrophic, sulfide-oxidizing bacteria. However, the range of possible metabolic pathways is very diversified, varying from the heterotrophy to the chemolithoautotrophy. Because of this huge variability the diverse bacteria of this genus can differ greatly from each other.

Carbon metabolism

In ''Beggiatoa'' group are present both autotrophic and heterotrophic metabolisms. Autotrophic ''Beggiatoa'' carry out the CO₂ fixation through the Calvin cycle and the employment of the RuBisCO enzyme. The latter shows different regulation levels in obligated and facultative autotrophs. For instance, in the obligately autotrophic strain MS-81-1c RuBisCO cannot be repressed, while in the facultatively autotrophic strain MS-81-6 it is tightly regulated to switch from autotrophic to heterotrophic growth and vice versa. Beside the autotrophic strains, most of the freshwater ''Beggiatoa'' strains are heterotrophic, requiring organic substrates for growth. Specifically, many of them can be considered mixotrophs, because they grow heterotrophically, oxidizing organic compounds, but they can also use sulfide or other reduced sulfur compounds as electron donors. By this strategy, the organic carbon skeletons are saved for the purpose of increasing biomass and the CO₂ autotrophic fixation is not required. Mixotrophy has been suspected to be the trophic modality for many freshwater strains, but it has only been found in one marine strain of ''Beggiatoa'', MS-81-6. Also a metabolic pathway of C-1 compounds utilization has been revealed in Beggiatoa leptomitoformis strain D-402, through comprehensive analysis of its genomic, bochemistry, physiology and molecular biology.

Nitrogen metabolism

''Beggiatoa'' group shows substantial versatility in utilizing nitrogen compounds. Nitrogen can be a source for growth or, in the case of nitrate, it can be an electron acceptor for anaerobic respiration. Heterotrophic freshwater ''Beggiatoa'' spp. assimilate nitrogen for growth. Nitrogen sources include nitrate, nitrite, ammonia, amino acids, urea, aspartate, asparagine, alanine and thiourea, depending on the capability of specific strains.  

Autotrophic vacuolated ''Beggiatoa'' are able to store nitrate in their vacuoles 20.000 times the concentration of the surrounding sea water, and use it as terminal electron acceptor in anoxic conditions. This process, called Dissimilatory Nitrate Reduction to Ammonium (DNRA), reduces nitrate to ammonium. The capability of using nitrate as electron acceptor allows the colonization of anoxic environments, such as microbial mats and sediments. Several species are able to fix nitrogen using nitrogenase enzyme (e.g. ''Beggiatoa alba'').

Sulfur metabolism

One of the defining features of the genus ''Beggiatoa'' is the production of intracellular inclusions of sulfur resulting from the oxidation of reduced sulfur sources (e.g. hydrogen sulfide). In autotrophic ''Beggiatoa'', sulfide is a source of energy and electrons for carbon fixation and growth. The oxidation of sulfide can be aerobic or anaerobic, in fact it can be coupled with the reduction of oxygen or with the reduction of nitrate. Sulfur produced by the oxidation of sulfide is stored into internal globules and can be used when the concentration of sulfide decreases. Thus, the temporarily storing of elemental sulfur (S⁰) increase the adaptability of an organism and its tolerance to changes in the concentrations of sulfide and oxygen.

Sulfide aerobic oxidation:  H2S + 0,5O2 -> S^0 + H2O 

Sulfide anaerobic oxidation:  4H2S + NO3^- + 2H+ -> 4S^0 + NH4^+ + 3H2O

There are some cases of chemoorganotrophy, too. For instance, the strain ''Beggiatoa'' sp. 35Flor usually do an aerobic respiration coupled with the oxidation of sulfide, but in anoxic condition a different type of respiration is activated. The energy is gained chemoorganotrophically from oxidation of PHA (polyhydroxyalkanoates), organic compounds previously synthesized through CO₂ fixation during chemolithotrophic growth on oxygen and sulfide. In this case electron acceptor is the sulfur stored into the cell, so the final product is hydrogen sulfide.

Anaerobic respiration:  PHA + S^0 -> CO2 + H2S

Hydrogen metabolism

The strain ''Beggiatoa'' sp. 35Flor is able to use hydrogen as alternative electron donor to sulfide. This oxidation process can provide energy for maintenance and assimilatory purposes and is helpful to reduce stored sulfur when it becomes excessive, but it can't provide growth to the strain.

Hydrogen oxidation:  H2 + S^0 -> H2S

Phosphorus metabolism

''Beggiatoa''’s metabolism include the use of phosphorus in the polyphosphate form. The regulation of this metabolism relies on the environmental conditions. Oxygenated surroundings cause an accumulation of polyphosphate, while anoxia (coupled with an increasing concentration of sulfide) produces a breakdown of polyphosphate and its subsequent release from the cells. The released phosphate can then be deposited as phosphorite minerals in the sediments or stay dissolved in the water.

Ecology

Filaments have been observed to form dense mats on sediments in a very huge variety of environments. They appear as a whitish layer and since they are present and flourish in marine environments which have been subject to pollution, they can be considered as an indicator species. ''Beggiatoa'' and other related filamentous bacteria can cause settling problems in sewage treatment plants, industrial waste lagoons in canning, paper pulping, brewing, milling, causing the phenomenon called " bulking". ''Beggiatoa'' are also able to detoxify hydrogen sulfide in soil and have a role in the immobilization of heavy metals.

''Beggiatoa'' live at the oxic/anoxic interface, where they benefits from the presence of both hydrogen sulfide and oxygen. The chemolithoautotrophic strains of ''Beggiatoa'' are also considered important primary producers in dark environments.

Habitat

The incredible number of adaptations and metabolisms of this genus of bacteria are consequences of the extraordinary environmental variability they can live in. ''Beggiatoa'' is almost benthic, it can be found in marine (''Beggiatoa'' sp''.'' MS-81-6 and MS-81-1c) or freshwater (''Beggiatoa alba'') environments and they only need sulfide or thiosulfide as electron donor and an oxidizer. They can usually be found in habitats that have high levels of hydrogen sulfide, these environments include cold seeps, sulfur springs, sewage contaminated water, mud layers of lakes, and near deep hydrothermal vents. ''Beggiatoa'' can also be found in the  rhizosphere of swamp plants, in soil, marine sediments and in the mangrove lagoon too (where they contribute to the lipid pool of the sediments). The freshwater species have typical habitats in sulfur springs, ditches, puddles, wetlands, lake sediments and in rice fields, where it can grow associated with the rice plants’ roots. The ''Beggiatoa'' that live in marine water can be found in regions where their source of energy (sulfide or thiosulfide) is available. It can be extracted from both inorganic or organic source and usually it is coupled with microoxic