Differential Habitat Use and Niche Partitioning by Pseudomonas Species in Human Homes

Abstract

Many species of Pseudomonas have the ability to use a variety of resources and habitats, and as a result Pseudomonas are often characterized as having broad fundamental niches. We questioned whether actual habitat use by Pseudomonas species is equally broad. To do this, we sampled extensively to describe the biogeography of Pseudomonas within the human home, which presents a wide variety of habitats for microbes that live in close proximity to humans but are not part of the human flora, and for microbes that are opportunistic pathogens, such as Pseudomonas aeruginosa. From 960 samples taken in 20 homes, we obtained 163 Pseudomonas isolates. The most prevalent based on identification using the SepsiTest BLAST analysis of 16S rRNA (http://www.sepsitest-blast.de) were Pseudomonas monteilii (42 isolates), Pseudomonas plecoglossicida, Pseudomonas fulva, and P. aeruginosa (approximately 25 each). Of these, all but P. fulva differed in recovery rates among evaluated habitat types (drains, soils, water, internal vertebrate sites, vertebrate skin, inanimate surfaces, and garbage/compost) and all four species also differed in recovery rates among subcategories of habitat types (e.g., types of soils or drains). We also found that at both levels of habitat resolution, each of these six most common species (the four above plus Pseudomonas putida and Pseudomonas oryzihabitans) were over- or under-represented in some habitats relative to their contributions to the total Pseudomonas collected across all habitats. This pattern is consistent with niche partitioning. These results suggest that, whereas Pseudomonas are often characterized as generalists with broad fundamental niches, these species in fact have more restricted realized niches. Furthermore, niche partitioning driven by competition among Pseudomonas species may be contributing to the observed variability in habitat use by Pseudomonas in this system.

Infection Prevention and Control Guideline for Cystic Fibrosis: 2013 Update

“…In the homes of people without CF, P. aeruginosa was detected most often from kitchen and bathroom drains but not from soil. 304 Similarly, in the homes of people with CF, P. aeruginosa was detected most often from shower drains and bathroom drainpipes. 305,306 While P. aeruginosa was recovered from 34% of the homes of newly infected people with CF (6% of samples), only 9 (18%) of 50 paired environmental and patient isolates were the same strain.…”

Recovery and biogeography of Pseudomonas and Burkholderia species from the human home.

“…There is some evidence to suggest that recovery of P. aeruginosa is higher for some types of drains (bathroom sinks), and the higher recovery from bathroom sink drains is consistent with other comparisons of P. aeruginosa in household drains (Remold et al 2011). However, most important is that P. aeruginosa recovery is highest for household drains.…”

“…These characteristics would indicate that as a genus Pseudomonas has a broad fundamental niche as defined by Hutchinson (1959). Consistent with this, Pseudomonas species have been isolated from a variety of habitats such as: soils and rhizospheres (Green et al 1974;Berg et al 2005), drains (Regnath et al 2004;Remold et al 2011), fresh water rivers (Pirnay et al 2005), open oceans (Kahn et al 2008), "petroleum sludge" (Bharali and Konwar 2011), insects (Saitou et al 2009), medical equipment (Srinivasan et al 2003),…”

“…In contrast, although P. aeruginosa was recovered from every home sampled (regardless of patient status), the patterns of recovery from these homes were not consistent with this species being ubiquitous in nature with respect to environment type. Rather, P. aeruginosa was primarily found in drains, consistent with Ojima, et al 2002, Regnath et al 2004, and Remold et al 2011.…”

“…aeruginosa is often referred to as "global" or "ubiquitous" (Goldberg 2000;Stover et al 2000). Even though P. aeruginosa has been isolated from many highly variable environments, only a few studies have examined it in environments or at a scale relevant to objects that young CF patients might contact on a daily basis (Mortensen et al 1995;Ojima et al 2002;Regnath et al 2004;Schelstraete et al 2008;Remold et al 2011). Four of these five studies (Mortensen et al 1995;Ojima et al 2002;Regnath et al 2004;Schelstraete et al 2008 …”