MicrobiologyBytes

What would happen if all the leaves fell off the trees and did not rot? We’d be buried under them and all plants would run out of nutrients and die, then we would starve. So the seemingly non-sexy buisness of rotting is rather important when it comes to element and nutrient cycles.

In ecological studies, leaf litter degradation is often estimated by measuring parameters such as soil respiration, litter mass loss or the activities of specific microbial enzymes in soil extracts. In microbiology, the degradation of plant-derived compounds such as lignocellulose has been studied using a few microbial model species and has recently led to the sequencing of the genomes of different saprotrophic fungal species which use different strategies to degrade plant material, thus revealing the full enzymatic machinery implicated in this process. Under natural conditions, litter degradation is generally carried out by consortia of species that either act simultaneously or replace one another on a common piece of plant debris in a sometimes predictable manner and not by a single microbial species. It can therefore be anticipated that the molecular machinery deployed to completely mineralize litter in the field is far more complex and diverse than the machinery observed in a single microbial genome. In addition, it is likely that the diversity of this machinery is partly controlled by litter chemistry and complexity and therefore by plant community composition.

By allowing access to the genome contents of the different microorganisms present in a common environment (metagenomics) or to the set of genes they express (metatranscriptomics), environmental genomics offers a novel opportunity to decipher at the molecular level, complex ecological processes such as plant organic matter degradation, thus bridging the gap between global field measurements and targeted genomic approaches.

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils. (2012) PLoS ONE 7(1): e28967. doi:10.1371/journal.pone.0028967
Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60%) and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5% (beech soil)–0.8% (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter.

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First it was foot and mouth virus.
Then it was bluetongue virus.
Now it is Schmallenberg virus.
So here’s 10 things you didn’t know about Schmallenberg virus:

1. Schmallenberg virus was first isolated in Schmallenberg, Germany, in November 2011.
2. Schmallenberg virus is a Bunyavirus, one of a large group of of negative-stranded RNA viruses.
3. Why should I care? In cows, Schmallenberg virus causes fever and a drastic reduction in milk production. In sheep it causes congenital malformations and stillborn lambs (also stillborn calves in cows).
4. Schmallenberg virus was first identifed in the UK on 23rd January 2012.
5. Like Bluetongue, Schmallenberg virus is transmitted by midges (Culicoides spp.), which means we will be unlikely to be able to eradicate it – vaccination of anaimals is the only likely effective response.
6. Where did Schmallenberg virus come from? The virus genome is most closely related to sequences of a different Orthobunyavirus called Shamonda virus which belongs to the so-called Simbu serogroup known to infect ruminants and be transmitted by midges. In other words, it has form. But whether it is newly evolved (unlikely) or just newly discovered we don’t yet know.
7. How did Schmallenberg virus reach the UK? We don’t know. It could have been due to animal movements, but since it was first identifed in eastern England, it’s possible that it arrived in midges travelling under their own steam.
8. Is Schmallenberg virus going to spread to other parts of the UK and other countries? Yes, you can bet on that (just like bluetongue did).
9. Can I catch Schmallenberg virus? Honest answer: We don’t know. Possibly, but there have been no reports of human illness from areas where the virus is known to exist, so I wouldn’t worry too much.
10. Where can I find the latest news about Schmallenberg virus? Right here.
11. OK, one last time, why should I care? Because Schmallenberg virus is going to cost European and probably worldwide ecomonies millions of pounds. And that will affect you.

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Oceans cover approximately 70% of Earth’s surface and play fundamental roles in processes that have global ecological and socioeconomic impacts. They are a vital component of the climate system and are suffering and partially attenuating climate change. Life originated in the oceans, which have been the main sites of evolution. Photosynthesis is a critical process that allows life on Earth, and interestingly, half the global primary production occurs in the sea, mostly by planktonic microorganisms that account for only 0.2% of global primary producer biomass. This has many consequences for the functioning of marine ecosystems, influencing carbon and energy fluxes through organisms (food webs), affecting carbon fluxes to deep waters (biological pump), and fine-tuning of all biogeochemical cycles.

Planktonic microorganisms are categorized into classes based on size for operational purposes. Initially, only prokaryotes were included in the smallest class (picoplankton: cells 0.2 to 2 μm) and microbial eukaryotes (protists) were included in the nanoplankton (2 to 20 μm) or microplankton (20 to 200 μm). However, minute eukaryotes were soon detected by epifluorescence microscopy and flow cytometry. Picoeukaryotes are now known to be ubiquitous in surface oceans and form, together with prokaryotes, an ocean’s veil above which larger protists and metazoans might bloom. They exemplify the ecological success of miniaturized cells prepared for independent life by keeping only the minimal cellular components, typically one mitochondrion, one Golgi apparatus, and optionally one chloroplast and flagellum. Molecular methods today offer new tools for studying picoplankton biogeography, activity, biological interactions, and population control mechanisms.

Eukaryotic picoplankton in surface oceans. Annu Rev Microbiol. (2011) 65: 91-110
The eukaryotic picoplankton is a heterogeneous collection of small protists 1 to 3 µm in size populating surface oceans at abundances of 10(^2) to 10(^4) cells ml(^1). Pigmented cells are important primary producers that are at the base of food webs. Colorless cells are mostly bacterivores and play key roles in channeling bacteria to higher trophic levels as well as in nutrient recycling. Mixotrophy and parasitism are relevant but less investigated trophic paths. Molecular surveys of picoeukaryotes have unveiled a large phylogenetic diversity and new lineages, and it is critical to understand the ecological and evolutionary significance of this large and novel diversity. A main goal is to assess how individuals are organized in taxonomic units and how they participate in ecological processes. Picoeukaryotes are convincingly integral members of marine ecosystems in terms of cell abundance, biomass, activity, and diversity and they play crucial roles in food webs and biogeochemical cycles.

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Cell-cell interactions are common to all living systems. Bacteria are no exception, and numerous mechanisms that use secreted products as signaling molecules are known. Among these, the so-called “quorum sensing” systems are perhaps the best studied. In quorum sensing, all bacterial cells within a population produce secreted molecules. Only when population densities are high is there a response to these compounds, thus allowing the bacteria to coordinate their behavior. However, it is clear that there is much more to bacterial cell–cell interactions than simply counting numbers and coordinating behavior. Secreted molecules also play key roles in microbial development so that different cell fates can arise and coexist within a single-species population. In addition, in settings where multiple species coexist, their interactions often are mediated through extracellular compounds. Development in one microbe can be influenced by small molecules secreted by other species.

Almost all quorum sensing studies have been performed under laboratory conditions – far removed from how bacteria actually live. What happens in the “wild” when rival bacterial gangs contest the same territory?

Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. PNAS USA November 10 2011. doi: 10.1073/pnas.11036301
Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals before entering sporulation. We investigated whether organisms from the natural environment of B. subtilis – the soil – were able to alter the development of B. subtilis. To test this possibility, we developed a coculture microcolony screen in which we used fluorescent reporters to identify soil bacteria able to induce matrix production in B. subtilis. Most of the bacteria that influence matrix production in B. subtilis are members of the genus Bacillus, suggesting that such interactions may be predominantly with close relatives. The interactions we observed were mediated via two different mechanisms. One resulted in increased expression of matrix genes via the activation of a sensor histidine kinase, KinD. The second was kinase independent and conceivably functions by altering the relative subpopulations of B. subtilis cell types by preferentially killing noncannibals. These two mechanisms were grouped according to the inducing strain’s relatedness to B. subtilis. Our results suggest that bacteria preferentially alter their development in response to secreted molecules from closely related bacteria and do so using mechanisms that depend on the phylogenetic relatedness of the interacting bacteria.

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As a new paper confirms the presence of thousands of “unknown” viruses in raw sewage, it brings to mind something we already knew – that although there are a lot of “unknown” viruses out there, most of them are tailed bacteriophages, blown apart, reshuffled and reassembled:

Raw Sewage Harbors Diverse Viral Populations. mBio 2 (5) e00180-11 4 October 2011 doi: 10.1128/​mBio.00180-11
At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity.

Analysis of the virus population present in equine faeces indicates the presence of hundreds of uncharacterized virus genomes. (2005) Virus Genes. 30(2): 151-156
Virus DNA was isolated from horse faeces and cloned in a sequence-independent fashion. 268 clones were sequenced and 178140 nucleotides of sequence obtained. Statistical analysis suggests the library contains 17560 distinct clones derived from up to 233 different virus genomes. TBLASTX analysis showed that 32% of the clones had significant identity to GenBank entries. Of these 63% were viral; 20% bacterial; 7% archaeal; 6% eukarya; and 5% were related to mobile genetic elements. Fifty-two percent of the virus identities were with Siphoviridae; 26% unclassified phages; 17% Myoviridae; 4% Podoviridae; and one clone (2%) was a vertebrate Orthopoxvirus. Genes coding for predicted virus structural proteins, proteases, glycosidases and nucleic acid-binding proteins were common.

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Many years ago in microbiology practical classes, we used to encourage students to smear bright red Serratia marcescens bacteria all over their hands so we could demonstrate principles of epidemiology and the spread of infection. At the time, this was believed to be a harmless marine bacterium, but we stopped when it gradually realised that this bug is not as harmless as we used to think. S. marcescens has been in the news recently as the cause of the highly contagious white pox disease which kills corals, but it has a wide host range that includes plants, insects and nematodes, and it is also an opportunistic pathogen of mammals including humans. A new paper in PLoS ONE reveals the way in which this bacterium invades human cells.

Serratia marcescens Is Able to Survive and Proliferate in Autophagic-Like Vacuoles inside Non-Phagocytic Cells. 2011 PLoS ONE 6(8): e24054. doi:10.1371/journal.pone.0024054
Serratia marcescens is an opportunistic human pathogen that represents a growing problem for public health, particularly in hospitalized or immunocompromised patients. However, little is known about factors and mechanisms that contribute to S. marcescens pathogenesis within its host. In this work, we explore the invasion process of this opportunistic pathogen to epithelial cells. We demonstrate that once internalized, Serratia is able not only to persist but also to multiply inside a large membrane-bound compartment. This structure displays autophagic-like features, acquiring LC3 and Rab7, markers described to be recruited throughout the progression of antibacterial autophagy. The majority of the autophagic-like vacuoles in which Serratia resides and proliferates are non-acidic and have no degradative properties, indicating that the bacteria are capable to either delay or prevent fusion with lysosomal compartments, altering the expected progression of autophagosome maturation. In addition, our results demonstrate that Serratia triggers a non-canonical autophagic process before internalization. These findings reveal that S. marcescens is able to manipulate the autophagic traffic, generating a suitable niche for survival and proliferation inside the host cell.

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In my time as a microbiology student, the nitrogen cycle was a staple of introductory microbiology classes (as it still is), and we all learned that nitrification, the process of converting harmful ammonia into less toxic nitrate was carried out by Nitrosomonas and Nitrobacter and that kept our goldfish alive.

Whaddya know? 30 years later I find out that … like many of the things we thought we knew back then … that was wrong.

Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters. 2011 PLoS ONE 6(8): e23281. doi:10.1371/journal.pone.0023281
Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.

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The world’s remaining 786 mountain gorillas (Gorilla beringei beringei) live in 2 parks in Rwanda, Uganda, and the Democratic Republic of the Congo. An ecotourism industry for viewing human-habituated mountain gorillas in the wild is thriving in all 3 countries. Mountain gorilla tourism helps ensure the sustainability of the species by generating much-needed revenue and increasing global awareness of the precarious status of this species in the wild. Tourism, however, also poses a risk for disease transmission from humans to the gorillas.

Habitat encroachment and poaching are threats to wildlife survival, particularly in the developing world. Mountain gorillas face an additional threat from infectious diseases. Second only to trauma, infectious diseases, primarily respiratory, account for 20% of sudden deaths. The close genetic relatedness of mountain gorillas and humans has led to concerns about the potential interspecies transmission of infectious agents. Although most surveillance efforts focus on risk for humans, mountain gorillas are immunologically naive and susceptible to infection with human pathogens. The parks in which mountain gorillas live are surrounded by the densest human populations in continental Africa. In addition, research and gorilla ecotourism brings thousands of persons from the local communities and from around the world into direct and indirect contact with the gorillas. The frequency and closeness of contact is particularly pronounced in Virunga National Park, where 75% of mountain gorillas are habituated to the presence of humans.

To minimize the threat of disease transmission, the Rwandan, Ugandan, and Congolese governments restrict tourist numbers and proximity, and the Congolese wildlife authority mandates that masks be worn by persons visiting gorillas. Nonetheless, the frequency and severity of respiratory disease outbreaks among mountain gorillas in the Virunga Massif have recently increased. From May through August 2008, sequential respiratory outbreaks occurred in 4 groups of mountain gorillas accustomed to tourism in Rwanda. Between June 28 and August 6, 2009, a fifth outbreak occurred in 1 of these groups, Hirwa. This paper describes the Hirwa outbreak. Respiratory outbreaks were defined as more than one third of animals in a group exhibiting signs of respiratory disease (coughing, oculonasal discharge, and/or lethargy).

Human metapneumovirus infection in wild mountain gorillas, Rwanda. Emerg Infect Dis. Apr 2011 doi: 10.3201/eid1704.100883
The genetic relatedness of mountain gorillas and humans has led to concerns about interspecies transmission of infectious agents. Human-to-gorilla transmission may explain human metapneumovirus in two wild mountain gorillas that died during a respiratory disease outbreak in Rwanda in 2009. Surveillance is needed to ensure survival of these critically endangered animals.

Related:

• Newly discovered respiratory viruses
• Molecular Epidemiology and Evolution of Human Respiratory Syncytial Virus and Human Metapneumovirus
• Human metapneumovirus glycoprotein G is an important virulence factor

I’m trying to persuade a student to do my final year project next year on badger culling and bovine tuberculosis:

Bovine tuberculosis (bTB) remains an important public health concern worldwide as a result of deficiencies in preventing and/or controlling measures targeting the spread of its causative agent Mycobacterium bovis. While the risk posed by M. bovis to human health is low in most developed countries, the main causes of concern related to M. bovis in industrialized countries are epizootics in domesticated and wild mammal populations. Infection with M. bovis remains a significant livestock zoonosis in the European Union where some member states experience a reemergence of the disease despite significant historical efforts to implement eradication plans. In Great Britain, the disease was eliminated from most cattle herds by 1960, with the exception of infection hotspots in southwest England, after the implementation of a herd testing and slaughter policy. However, efforts to completely eradicate bTB in Great Britain have been hampered by the maintenance of M. bovis in wildlife host populations, acting as reservoirs of infection, in particular badgers (Meles meles). Since 1979, incidence in British cattle has increased and the infection has become more geographically widespread. Over 7 million cattle were tested for bovine bTB in 2009 and one in ten herds experienced bTB-related movement restrictions during the year as a result of at least one member of the herd failing the tuberculin skin test or showing lesions consistent with bTB during the slaughterhouse inspection – an event known as a “herd breakdown”.

Local Cattle and Badger Populations Affect the Risk of Confirmed Tuberculosis in British Cattle Herds. 2011 PLoS ONE 6(3): e18058. doi:10.1371/journal.pone.0018058
Background: The control of bovine tuberculosis (bTB) remains a priority on the public health agenda in Great Britain, after launching in 1998 the Randomised Badger Culling Trial (RBCT) to evaluate the effectiveness of badger (Meles meles) culling as a control strategy. Our study complements previous analyses of the RBCT data (focusing on treatment effects) by presenting analyses of herd-level risks factors associated with the probability of a confirmed bTB breakdown in herds within each treatment: repeated widespread proactive culling, localized reactive culling and no culling (survey-only).
Methodology/Principal Findings: New cases of bTB breakdowns were monitored inside the RBCT areas from the end of the first proactive badger cull to one year after the last proactive cull. The risk of a herd bTB breakdown was modeled using logistic regression and proportional hazard models adjusting for local farm-level risk factors. Inside survey-only and reactive areas, increased numbers of active badger setts and cattle herds within 1500 m of a farm were associated with an increased bTB risk. Inside proactive areas, the number of M. bovis positive badgers initially culled within 1500 m of a farm was the strongest predictor of the risk of a confirmed bTB breakdown.
Conclusions/Significance: The use of herd-based models provide insights into how local cattle and badger populations affect the bTB breakdown risks of individual cattle herds in the absence of and in the presence of badger culling. These measures of local bTB risks could be integrated into a risk-based herd testing programme to improve the targeting of interventions aimed at reducing the risks of bTB transmission.

Related:

• Public health and bovine tuberculosis
• Culling badgers a low priority for curbing cattle tuberculosis
• Irish badger cull ‘futile’ in controlling bovine tuberculosis