Nature 2007, 449:843–849.PubMedlearn more CrossRef 6. van den Abbeele P, van de Wiele T, Verstraete W, Possemiers S: The host selects VX-770 in vitro mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiol Rev 2011, 35:681–704.PubMedCrossRef 7. Li XJ, Yue LY, Guan XF, Qiao SY: The adhesion of putative probiotic

lactobacilli to cultured epithelial cells and porcine intestinal mucus. J Appl Microb 2008, 104:1082–1091.CrossRef 8. Macfarlane S: Microbial biofilm communities in the gastrointestinal tract. J Clin Gastroenterol 2008,42(Suppl 3):S142-S143.PubMedCrossRef 9. Macfarlane S, Dillon JF: Microbial biofilms in the human gastrointestinal tract. J Appl Microbiol 2007, 102:1187–1196.PubMedCrossRef 10. Marzorati M, van den Abbeele P, Possemiers S, Benner J, Verstraete W, van de Wiele T: Studying the host-microbiota interaction in the human gastrointestinal

tract: basic concepts and in vitro approaches. Ann Microbiol 2011, 61:709–715.CrossRef 11. Molly K, Vande Woestyne M, de Smet J, Verstraete W: Validation of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) reactor using microorganism-associated activities. Microb Ecol Health Dis 1994, 7:191–200.CrossRef 12. Minekus M, Smeets-Peeters MJE, Bernalier A, Marol-Bonnin S, Havenaar R, Marteau P, Alric M, Fonty G, Huis in ’t Veld JHJ: A computer-controlled system to simulate conditions of the large intestine this website with peristaltic mixing, water absorption and absorption of fermentation products. Appl Microb Biotech 1999, very 53:108–114.CrossRef 13. Macfarlane GT, Macfarlane S: Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut. Curr Opin

Biotechnol 2005, 18:156–162.CrossRef 14. Venema K, van den Abbeele P: Experimental models of the gut microbiome. Best Pract Res Clin Gastroenterol 2013, 27:115–126.PubMedCrossRef 15. Marzorati M, Possemiers S, Verstraete W: The use of the SHIME-related technology platform to assess the efficacy of pre- and probiotics. Agro Food Ind Hi-Tech 2009, 20:S50-S55. 16. Yoo MJY, Chen XD: GIT physicochemical modeling – a critical review. Int J Food Eng 2006,2(art):4. 17. Cinquin C, le Blay G, Fliss I, Lacroix C: Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model. Microb Ecol 2004, 48:128–138.PubMedCrossRef 18. Cinquin C, le Blay G, Fliss I, Lacroix C: New three-stage in vitro model for infant colonic fermentation with immobilized fecal microbiota. FEMS Microbiol Ecol 2006, 57:324–336.PubMedCrossRef 19. Probert HM, Gibson GR: Bacterial biofilms in the human gastrointestinal tract. Curr Issues Intest Microbiol 2002, 3:23–27.PubMed 20. Macfarlane S, Woodmansey EJ, Macfarlane GT: Colonization of mucin by human intestinal bacteria and establishment of biofilm communities in a two-stage continuous culture system. Appl Environ Microbiol 2005, 71:7483–7492.PubMedCentralPubMedCrossRef 21.

5 kb PCR and semi-nested BMS345541 cell line PCR applied to DNA of cultured of Coccidioides spp. and controls Direct PCR with primers specific for Coccidioides spp. (RFA12/P2) was able to identify 19 out of the

21 Coccidioides spp. isolates tested, which presented the specific 375-bp band. However, semi-nested PCR using the same primers, RFA12/RFA13 and RFA12/P2, was able to identify all the 21 isolates tested (Figures 1 and 2). The same direct and semi-nested PCR methodologies presented negative SP600125 chemical structure results when applied to DNA of all species of other different pathogenic fungi and bacteria. These results demonstrate the high specificity of the primers developed in this study and highlight the increased sensitivity, expected in semi-nested PCR reactions from environmental samples. Figure 1 1.2% agarose gel showing results of semi-nested PCR with primers RFA12/RFA13 and RFA12/P2 specifics for Coccidioides spp., lines 1-4 DNA isolated of C. immitis (US), lines 5-9 DNA isolated of C. posadasii (Piauí/Brazil), and line 10 negative control (DNA C. neoformans ). MW = 1 Kb DNA Ladder (Promega).

Figure 2 1.2% agarose gel showing results of semi-nested PCR with primers RFA12/RFA13 and RFA12/P2 specifics for Coccidioides spp. lines 1-2 DNAs Rhodococcus equi 33701 e Mycobacterium avium 13956, lines GW-572016 cost 3-4 DNA isolated of C. immitis (US), lines 5-6 DNA isolated of C. posadasii (Argentina) and lines 7-13 DNA isolated of C. posadasii (Piauí/Brazil) MW = 1 Kb DNA Ladder (Promega). PCR and semi-nested PCR applied to soil DNA samples The DNA obtained from the soil samples was submitted to direct PCR and

semi-nested PCR using the same primer system. Only 8 out of 24 (33.3%) soil samples presented the specific 375-bp band by direct PCR: 2/10 from Elesbão Veloso and 6/14 from Caridade do Piauí (Data not shown). However, using semi-nested PCR with the primers RFA12/RFA13 and RFA12/P2, all the soil samples presented the specific 375-bp Neratinib band indicative of Coccidioides spp. (Figure 3). By the same molecular method, the DNA obtained from the soil of central Brazil presented 100% negative results. The results comparing both classical and molecular methods to detect Coccidioides spp. in soil samples are summarized in Table 1. Figure 3 1.2% agarose gel showing results of semi-nested PCR with primers RFA12/RFA13 and RFA12/P2 specific for Coccidioides spp., lines 2-11 soil samples from Elesbão Veloso (EV), lines 12 and 13 Caridade do Piauí (CP). Line 1 = white and MW = 1 Kb DNA Ladder (Promega). Table 1 Detection of C. posadasi i in soil samples by classical and molecular methods in Piauí, Brazil.

Importantly, the large number of unclassifiable short reads observed previously was reduced to <100 sequences when the HBDB was included in the training set (Figure 2B) and the average bootstrap scores for these classifications were generally above 90% (Figure 2B). When we classify these short reads using the HBDB alone (that is, without the inclusion of existing training

sets), we see a similar result – the majority of the sequences are classified at a 60% bootstrap threshold (Figure 2C). VX-765 mouse However, without the additional breadth provided by the GG, SILVA, or RDP training sets, nearly 15% of the short reads (650 out of a total of 4,480) are unclassifiable and average bootstrap scores drop in value, suggesting that the diversity within the bee gut has not been exhaustively characterized by previous 16S rRNA clone library based studies. In contrast to the classifications provided by the published training sets BLZ945 mw alone (where only 62% of the classifications agreed at the family level across all three training sets), the inclusion of the bee specific sequences dramatically increased the congruence (94% of the sequences agreed at the family level, Table 1). For particular taxonomic

orders with high representation (>100 unique sequences) in the honey bee gut, there are particularly few incongruences at the Family level (Figure 2B). Only the RDP + bees training set identifies sequences as Orbus classified as either Gamma-1 or Enterobacteriales by the GG + bees or SILVA + bees training sets. It is possible that this error is due to the fact that the RDP training set was the smallest included

in this comparative analysis; size and diversity of the training set affects the resulting assignments [11]. We utilized an evolutionary placement algorithm implemented in RAxML to identify the phylogenetic position of short reads classified as Orbus by the RDP + bees training set. selleck chemical Indeed, these Orbus-like sequences clade within the gamma-1 group (Additional file 1). The spurious placement of these short reads within Orbus by RDP was therefore primarily due to the fact that Orbus is the closest sequence to gamma-1 found within the RDP training set. Biological significance In the end, the goal Cyclic nucleotide phosphodiesterase of the classifications provided by the RDP-NBC for next generation sequencing datasets is to provide a sense of community structure that may be relevant to function in the environment. There were few incongruities between the HBDB-based taxonomies and those in the existing training sets, primarily because existing training sets did not include sequences identical to these bee-specific groups. Across all three training sets, only 14 sequences were found to be identical to those in the HBDB. The Greengenes training set, for example, included the majority of these identical sequences (12/14) and many closely related sequences (>95% identical across the full length) Additional file 2).

Photosynth Res 73(1–3):149–156PubMedCrossRef Portis AR Jr, PRT062607 clinical trial Parry MAJ (2007) Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective. Photosynth

Res 94(1):121–143PubMedCrossRef Portis AR Jr, Salvucci ME (2002) The discovery of rubisco activase—yet another story of serendipity. Photosynth Res 73(1–3):257–264CrossRef Prasil O, Suggett DJ, Cullen JJ, Babin M, Govindjee (2008) Aquafluo 2007: chlorophyll fluorescence in aquatic sciences, an international conference held in Nové Hrady. Photosynth Res 95(1):111–115PubMedCrossRef Prince RC (1992) Robert Hill, FRS; his published work. Photosynth Res 34(3):329–332CrossRef Putnam-Evans C, Barry B (eds) (2007) Photosynthetic water oxidation. Photosynth Res 92(3):273–425 Rabinowitch E (1961) Robert Emerson (1903–1959). Biogr Mem Natl Acad Sci USA 25:112–131 Rabinowitch A (2005) Founder and father. Bull At Sci 61(1):30–37CrossRef Raghavendra

AS, Sane PV, Mohanty P (2003) Photosynthesis research in India: transition from yield physiology into molecular biology. Photosynth Res 76(1–3):435–450PubMedCrossRef Rao KK (1999) David Hall (1935–1999). Photosynth Res 62(2):117–119CrossRef Rebeiz CA, Benning C, Bohnert H, Hoober JK, Portis AR (2007) Govindjee was honored with the first lifetime achievement award, and Britta Förster and coworkers, with the first annual paper prize of Rebeiz foundation for basic research. Photosynth Res 94(1):147–151CrossRef Renger G (1987) Conference report on the Japan/US-binational seminar on “energy conversion: photochemical reaction centers and Selleckchem Avapritinib oxygen evolving complexes of plant photosynthesis”. Photosynth Res 13(3):261–MG-132 order 268CrossRef Renger G (2003) Apparatus and mechanism of photosynthetic oxygen evolution: a personal perspective. Photosynth Res 76(1–3):269–288PubMedCrossRef Renger G (2008) Horst Tobias Witt (March 1, 1922–May

14, 2007). Photosynth Res 96(1):5–8CrossRef Rich PR (1992) Robin Hill: a personal perspective. Photosynth Res 34(3):333–335CrossRef Rich PR (ed) (1992) Robin Hill. Photosynth Res 34(3):319–488 Rieppel O (1985) The dream of Charles Bonnet (1720–1793). Gesnerus 42(3–4):359–367PubMed Rippka R (2003) Germaine Bcl-w Stanier (Cohen-Bazire) 1920–2001. Arch Hydrobiol-Suppl 148:17–34 Rochaix J-D (2002) The three genomes of Chlamydomonas. Photosynth Res 73(1–3):285–293PubMedCrossRef Rodermel S, Viret JF, Krebbers E (2005) Lawrence Bogorad (1921–2003), a pioneer in photosynthesis research: a tribute. Photosynth Res 83(1):17–24PubMedCrossRef Rosenberg JL (2004) The contributions of James Franck to photosynthesis research: a tribute. Photosynth Res 80(1–3):71–76PubMedCrossRef Rotblatt J (2000) Fifty Pugwash conferences: a tribute to Eugene Rabinowitch. Available online at: http://​www.​pugwash.​org/​reports/​pac/​pac256/​rotblat.​htm) Rurainski HJ (2004) The conference at Airlie House in 1963.

I will define here a living learn more organism as an entity formed by the functional integration of several “organs”, corresponding to the structure and functions of Lwoff’s definition. By analogy with multicellular organisms that are composed of several organs (skin, liver, brain and so on), unicellular

organisms can be defined as composed of several molecular machines and/or structures (metabolic networks, ribosomes, replicons, capsid, membranes and so on). A living organism can thus be defined as: “a collection of integrated organs (molecular machines/structures) producing individuals evolving through natural selection”. The simplest viruses encode two different “organs”, a replicon, allowing genome multiplication, and a capsid, i.e. a complex structure allowing not only to protect the viral genome in the extracellular space, but also involved in the entrance and exit mechanisms of virions in and out of the cell. All viruses encode selleck chemicals sophisticated mechanisms to divert the organs of the infected cells, such that these organs become part of the viral organism during infection. One can try to use our definition of organisms to approach the problem of the origin of life itself. Modern cells descending from LUCA and their viruses are all complex organisms, and LUCA PF-4708671 nmr itself has been the product of a long history (for a recent

review, see Forterre and Gribaldo 2007). Life

indeed Amrubicin already existed before the emergence of capsids and ribosomes. This is the reason why I included the ancestors of LUCA in my definition of life. At some point one should have to imagine the nature of primitive cells to include their features in our definition. The precise moment when life originated corresponds to the appearance of the first individuals formed by at least two integrated molecular organs (possibly a primitive metabolic network and a membrane) co-evolving through natural selection. Although the definition of life is a philosophical question, the choice of a definition has a great impact in the definition of scientific programs. The definition of life proposed here implies that the goal of biology should be to explore and understand exhaustively (via combining reductionist and integrative approaches) the mode of existence of living organisms and to understand their history (evolution being the cornerstone of biology). Above all, a program to study “the origin of life” should focus on looking, theoretically and experimentally, for the mechanisms that led to the emergence of the first living organisms on our planet. Acknowledgments I thank Michel Morange for the invitation to participate to the 2008 meeting on life definition in Paris. I am grateful to David Prangishvili, Didier Raoult and Simonetta Gribaldo for fruitful discussions.

Our data indicate that both strains influenced IEC-DC crosstalk with distinct outcomes compared to those induced by SupMODE. In particular, these strains markedly enhanced the expression of co-stimulatory markers and downregulated IL-12, TNF-α and IL-10 secretions by mDCs. In addition, similar alterations were induced by SupOLL2809 and SupL13-Ia, thus excluding a synergistic effect of IECs. However, our model does not allow us to further elucidate this probiotic activity this website because MODE-K cells do not form a confluent monolayer, instrumental to analyze the different roles played by paracellular and transcytosis pathways [42]. Taken together, our data suggest that the

L. gasseri influence on IEC-DC crosstalk is dominant over IEC activity. Importantly, MODE-K cells and L. gasseri are able to produce different outcomes, regulatory mDCs and “low-responsive” mDCs, respectively. Another beneficial effect on host immunity arising from the interaction between epithelia Abemaciclib cell line and commensal bacteria is the generation of reactive oxygen species that may activate the Nrf2 pathway and lead to improved antioxidant/detoxifying defenses [6]. The Nrf2-Keap1 complex serves as an intracellular oxidative stress sensor, and Nrf2 release, triggered by mild ROS production, activates the synthesis of a battery of cytoprotective/defensive proteins including GSH, GST and NQO1 that protect cells against oxidative stress and promote cell survival [5]. GSH plays

a key role in the maintenance and regulation of the cell’s redox status. Our data showing opposing effects of bacterial strains on MODE-K cells’ and DCs’ intracellular GSH content are consistent with the reported pro-oxidant activity exhibited by probiotic strains [6] and with the improved ability of DCs to Selleckchem TSA HDAC survive in an oxidant-rich environment [43]. Under normal conditions, intracellular GSH levels depend upon the rates of GSH synthesis/oxidation and on GSH export from cells, and the GSH/GSSG pair is widely used as an indicator of redox status. Data from this study on MODE-K cells, Mirabegron according to the literature, indicates that the lack of intracellular GSSG accumulation is associated with depletion and

increased export of intracellular GSH [44]. In contrast, the increased intracellular GSH concentration accompanied by the increase in GSHtot export from the DCs without any measurable raise of intracellular GSSG concentration indicates the ability of DCs to respond to L. gasseri-induced oxidative stress by increasing GSH synthesis. These results, along with the results showing the improvement of GST and NQO1 activities in DCs directly exposed to L. gasseri strains or to conditioned supernatants from MODE-K cells, along with in vivo studies, further support the ability of bacterial strains to activate the Nrf-2 pathway [8, 9]. Conclusions We have demonstrated in vitro differential immunomodulatory activities of two probiotic strains of L. gasseri, isolated from different sources.

Melanospheres were highly tumorigenic when injected subcutaneously in NOD Scid or Nude mice and all samples displayed tumor take of 100% down to 25000 cells. For one sample we performed a limiting dilution experiment and even as low as 5 cells readily generated buy GSK1120212 a tumor within 8 weeks (Figure 1B and C). In contrast, melanosphere-derived differentiated cells displayed

a decreased and delayed tumor growth in vivo, and as many as 5×104 differentiated cells generated a slowly growing tumor with a 10-week delay post-injection (Figure 1B). Immunohistochemical analysis of melanosphere-derived xenografts, performed for all samples, revealed a high similarity between the xenograft and the original patient tumor in terms of morphology and expression of the melanoma-associated diagnostic antigens MART1 and S100 (Figure 1D is a representative Alpelisib image). Following xenograft dissociation and re-injection we easily obtained secondary and tertiary tumors, suggesting that tumorigenic potential was not lost with passages in mice, in fact these results proved the ability of tumorigenic cells to self-renew in vivo (results not shown). Based on these in vitro and in vivo results, we considered melanospheres as surrogate of melanoma-initiating cells (MIC) exploitable for pre-clinical experimentation.

Melanospheres are resistant to chemotherapeutic drugs and to most pathway inhibitors We investigated the response of melaospheres to chemotherapeutic agents currently used in the treatment of melanoma patients. Melanospheres were exposed to cisplatin, temozolomide, dacarbazine and paclitaxel for 48 hours and cell viability was assessed by MTT assay. Overall a weak cytotoxic effect (<40% in all samples and with all drugs) was observed with Glycogen branching enzyme no therapeutic window as compared to normal melanocytes (Figure 2A). Conversely, differentiated cells were extremely sensitive to cisplatin, in 3 out of 3 samples assessed (Figure 2B is a representative sample). Figure 2 Drug resistance of melanosphere and pathway

activation. A) Cell viability of undifferentiated melanospheres of the indicated samples and melanocytes treated with the indicated drugs. Mean ± SD of 3 independent click here experiments is shown. ** p < 0,01. B) Cell viability of melanospheres (undifferentiated) and their progeny (differentiated) exposed to the indicated chemotherapeutic agents. A representative sample is shown. Mean ± SD of 3 independent experiments is shown. *** p < 0,001. C) Cell viability of melanospheres exposed to the indicated kinase inhibitors. Mean ± SD of 3 independent experiments is shown. ** p < 0,01; * p < 0,05 D) Immunoblot analysis of the indicated proteins or phosphoproteins in melanospheres. U251 and T98G glioblastoma cell lines were used as p-ERK positive and negative control, respectively.

“The new generations get educated, and they live in the towns,” an Ababda man of the Haranab clan explained. “The school education is not like the Arab traditional education. Elders who teach and give the first lessons on the desert are gone. “An Ababda of the Blalab clan added

that the educated children that live in the town “cannot live in the desert any more.” Most of our informants concur that once their kinsmen have settled down and adopted these new knowledge systems they do not return to desert life. It is remarkable that JNJ-64619178 supplier in recent years, many central Saharan nomads have chosen to remain in the desert explicitly because they have seen those who settle lose their desert knowledge, become poor, and find themselves unable to fall back on to the security provided by traditional knowledge and skills. Jeremy Keenan writes that “’the

failure of modernization to deliver find more on its promises’ is leading to a degree of nomadic cultural revivalism across much of the central Sahara” (Keenan 2006 p. 705). For our study area, we have only speculated whether abundant rains, the decline of tourism, political events or other variables might lead to a similar resurgence or restoration of desert-rooted livelihoods. Well informed decision making about desert development could also play a role. Conclusion Our research in a large area of the RSH reveals that tribal pastoral nomadic peoples with different ethnic and cultural roots have developed analogous ecological knowledge about how to manage their vital acacia resources with optimal efficiency. Through the generations they have passed that learning down as what we recognize as traditional ecological knowledge. This TEK has helped them to develop sustainable Vitamin B12 indigenous resource management strategies and tactics protecting the vital services of this ecological keystone species and thereby enabling their life in the desert. These peoples have a rich body of cultural associations with acacias that also generally help to safeguard the trees. The acacia

is a cultural keystone whose attributes draw from and contribute to the social, spiritual and moral characteristics of people who value the tree. Acacia management has long played a central role in moulding and maintaining the cultural landscapes of the RSH. These landscapes represent an enduring and S63845 datasheet largely successful human relationship with nature. Ongoing detrimental changes affecting acacia populations in the study area correlate more strongly with social impacts than with climatic factors. Social and economic pressures on cultural and natural resources are severing the intimate bonds between nature and nomadic culture. Ongoing social and economic changes and sedentarization among nomads may have strong and lasting environmental costs. Understanding and addressing these linkages are critical challenges for social and natural scientists and policy makers.

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7 %), Peltodytes casus (4.6 %) and Hydroglyphus hamulatus (4.3 %). Considering the average selleck inhibitor number of representatives of a given species per sample obtained from a particular type of pond, the most numerous species in clay pits were N. crassicornis (on average 1.87 individual per sample), L. minutus (1.42), L. minutus see more (1.1) and S. halensis (0.9). These values are much higher when samples in which a given species did not

occur are excluded (Online Appendix). The most numerous species in gravel pits were L. minutus (on average 2.81 individuals per sample) and L. minutus (0.59). The number of beetles (N) in particular ponds was strongly correlated with the species richness (S), both in clay pits (R = 0.79, p = 0.0001), and in gravel pits filled with water (R = 0.9, p = 0.0001). Correlations between the number of individuals N and values of the Shannon–Weaver index (H′) in particular types of the studied ponds proved to be non-significant (Spearman R, p < 0.05). The beetles dwelling in the analyzed ponds are characterized by high synecological diversity. Four groups of species can be distinguished (Pakulnicka 2008): eurytopic (54.1 % of all determined species), rheophilous (18.8 %), tyrphophilous (14.1 %) and argillophilous click here beetles (12.9 %) (Online Appendix). Counts of all the distinguished

groups, except argillophiles, are significantly different between clay and gravel pits (Mann–Whitney test, p < 0.05) and between ponds representing different succession stages (Kruskal–Wallis test, p < 0.05). These three groups of beetles demonstrate a strong correlation

with the type of bottom substrate (Spearman R, p < 0.05). Analysis of the relationships between Coleoptera and environmental factors Based on the conducted PCA analysis and correlation matrix between selected biocoenotic indices and observed environmental parameters, certain correlations were observed that can be described as significant to the formation of beetle fauna in clay and gravel pits. Undoubtedly, water temperature is a factor which strongly affects the counts of beetles inhabiting clay pits, their species richness 4��8C (S) and the value of the Shannon–Weaver index (H′) (r = −0.46, p < 0.05); these three characteristics are affected by CO3 2−,CO2, PO4-P or Cl− (Fig. 2a). Apart from water temperature, NH4-N, total N, BOD5 and HCO3 − are significant factors in the waters of gravel pits (Fig. 2b). Fig. 2 The principal component analysis (PCA) ordination plot of abundance, richness and diversity of water beetles colonizing clay pits (a) and gravel pits (b) in relation to the environmental variables in samples along the first and second PCA axis The physical and chemical parameters of water also have a significant impact on the formation of synecological assemblages. A strong relation was determined in clay pits between eurytopic, rheophilous and argillophilous beetles versus conductivity, SO4 2− and Cl−, and between rheophilous beetles versus NH4-N, Porg and BOD5 (Fig. 3a).