1. Introduction
Molecular sources are increasingly considered relevant in archaeological research. Besides the classical typology of human artefacts − pottery, tools, weapons and so on − organic residues and biomolecular markers are able to supply important information about early human populations or on the history or prehistory of ancient settlements or other places related to former human activities. Among other molecular markers, ancient DNA is particularly well suited for the identification and characterization of ancient human residues or residues of plants and animals [
1,
2,
3,
4]. The analysis of ancient DNA made it possible, for example, to reconstruct prehistoric migration processes [
5], to identify the ancient cultivation of plants [
6], or to detect the role of parasites in medieval cities [
7].
In addition to the analysis of DNA originating from multicellular organisms, the characteristic DNA of microorganisms can help to illuminate ancient life conditions and the effect of diseases on the development of human populations. Thus, the importance of pathogenic bacteria as the
Yersinia pestis which is known for the dramatic role they played during the middle ages could be understood for prehistoric populations, too [
8].
Besides genetic data originating from humans or from pathogens, the genetic composition of soil bacterial communities can have been affected by human activities and, therefore, carry information on the ancient situation of a prehistoric or historic settlement or work place [
9,
10]. This information is of high interest for archaeologists, for reconstruction of use of places and ancient local environmental conditions and the interactions between human activities as land use, settlements, handcraft and livestock farming with soil, on the one hand. On the other hand, the understanding of ancient human impact on soil bacterial community could open new insights into long-term ecological processes in soils as well as into the possible consequences of human activities on local ecological situations after centuries and millennia.
The composition of communities of soil bacteria can vary very strongly and is often marked by a very high diversity [
11]. It depends on the soil pH, salt content, humidity, nutrients and other chemical conditions and is influenced by the fate of a place in the past [
12]. Changing environmental conditions mean, in general, a change in the dominance of growing bacteria in soil. But, such changes do not mean a total and immediate disappearing of all bacteria growing before the environment changes. In opposite, some of the formerly growing bacteria might switch into a dormant state, to form spores and are reduced in their concentration, but can remain be present to a certain extend for a long time. Therefore, the composition of soil bacteria has not only to be understood as a mirror of the recent ecological situation of a place, but can also be interpreted as an “ecological memory” conserving information on former local ecological conditions [
13,
14]. This point of view makes analyses of local soil bacteria communities interesting for archaeology. Recent studies suggest the effect of former local human impact on soil bacteria situation [
15,
16], for example, for an iron age settlement [
17] and iron age burials [
18], for prehistoric hillforts [
19], for pre-industrial mining activities [
20] and a historical tannery site [
21]. From an archaeological point of view, a “biological memory of soil” was recognized in 2008 during the investigation of mycobiota in cultural layers of a medieval urban city and the term “soil mycological memory” was proposed [
22]. The concept of ecological memory was applied for describing [
23] and understanding the dynamics of interactions in communities over longer timescales [
24]. Paleoecological investigations suggest ecological memory effects at millennial time scales [
25]. By means of memory effects in simulations it seems to be possible to estimate the effect of perturbations on ecosystems and their resilence [
26]. Memory effects in soil are in the focus of interest due to their practical consequences for agriculture [
27]. Therefore, the composition of soil bacterial communities is particular important [
28]. Thus, short-term memory effects in top soil related to ecological dynamics in humus and soil fertility [
29,
30] as well as long-term biogeocenotic functions of microorganisms and the response behavior of soil microbiota on perturbations are important factors reflecting the role of ecological memory effects on different time scales which is interesting for archaeology, but also important for future measures in response to changing ecosystems and under climate and other anthropogenically caused stress [
31].
Beside the above mentioned recent investigations, published results of investigations on soil bacteria of archaeological soil samples are comparatively rare. But, data of soil bacteria compositions can include a lot of information concerning the state and the history of soil. This concerns recent chemical and nutritional conditions which are still influenced by changing composition of non-biological soil components in the past, on the one hand. They can include considerable effects as salt content, soil pH, gas permeability and oxygen availability, organic residues or presence of different nitrogen and sulfur species. On the other hand, it has to be taken in mind that formerly active bacteria could be conserved in soil pores in a less active or completely dormant state. This way, genetic information of soil bacteria components which had been active hundreds or thousands years ago could be stored in the covered soil and mirroring aspects of formerly local environmental conditions. This idea is based on the fact that changing environmental conditions cause changes of bacterial growth and shift the compositions of soil bacterial communities, but does not have to be responsible for an immediate disappearing of bacteria disadvantaged by change. In contrast, it is assumed, that dormant states of bacteria are stabilized and stored after re-locations of soil material and after covering of surface soil layers by other soil material, residues of buildings or deposition of other material on top during the changing use of a place in the past.
The present study is based on 16S rRNA analyses and shows considerable differences in soil bacteria composition at minor spatial distances. The series of soil samples from an archaeological excavation in the ancient city of Carnuntum (Austria) [
32] offered the possibility to investigate soil bacteria communities from different functional and temporal archaeological contexts from one place. 40 samples taken from different horizons and well-defined specific locations with different ancient functions gave the unique opportunity to compare soil bacterial communities, to analyzing them for similarities and searching for specific types. These samples seemed to be very interesting for looking for indications contradicting or confirming the concept of “ecological memory of soil”. In addition, such an analysis was motivated by the idea of a model study for checking the potential of the genetic data of soil bacteria for supplementing of archaeological findings and conclusions. Here, the results of the analysis of the 16S rRNA of this sample set are reported.
4. OTU Patterns of Single Samples
In this section, the sequencing results of the forty investigated single soil samples are discussed by the appearance of dominant OTUs on the one hand and exclusive OTUs on the other hand. It is assumed that the group of dominant OTUs might be related to antique human impact, but reflects mostly the recent ecological situation in the soil sample, which results from a superposition of ancient soil formation and deposition, recent processes in the soil and the development of soil situation in the intermediate time. In contrast, among the minor components of soil bacterial community OTUs are expected which are stronger related to the ancient ecological situation. With respect to the fact, that the soils of the single sampling spots of the whole excavation area experienced nearly the same fate since the late Roman Empire period it is supposed, that in particular types which are found exclusively or nearly exclusively in one sample can reflect the specific ecological situation in the phase before or during the deposition of soil material in the Antiquity. Thus, the list below includes OTUs with lower read numbers despite the fact that some remaining uncertainty has to be taken in mind.
C111; Hz D, first half 3rd century, soil fill in courtyard area: The soil bacterial community represented in the 16S rRNA data (SBC) is dominated by
Nocardioides (17.8 %),
Paenibacillus (5.1 %),
Bacillus (4.7 %) and
Burkholderiales TRA3-20 (4.4 %). Among a few exclusive strains, there were registered 27 reads of uncultivated
Chlamydiaceae and 8 reads of
Yuhusiella, a thermotolerant actinobacterium first isolated from a desert region in western China [
89]. Four other genera (
Oceaniovalibus, Gelidibacter, Proteinophilum and
Limosilactobacillus) have been found (33 – 88 read) nearly exclusive in C111.
Oceaniovalibus belongs to
Alphaproteobacteria and was first isolated from surface sea water near Taiwan [
90].
Gelidibacter was described as a seawater bacterium, too [
91].
Proteiniphilum is a strictly anaerobic proteinolytic bacterium found in the sludge of brewery waste water [
92].
Limosilactobacillus is a thermophilic bacterium. Strains of these genera have been isolated, for example, from human urine [
93]. The appearance of these OTUs could be interpreted as a signature related to an environment with enhanced salt content and protein-rich wastes.
C119: Hz D, soil fill under street surface, shortly after 200 AD.:
Pseudonocardia is with more than 15% of all reads the clearly dominant genus of the bacterial community. The sample supplied five exclusive OTUs with considerable read numbers between 110 and 173. Among them are
Pseudoglutamicibacter, the carotinoid dye-producing
Bizionia and
Saccharofermentans, an anaerobic bacterium first isolated from brewery wastewater [
94].
C124: Hz D, clayey fill inside building, deposited around 200 AD.: The bacterial community is dominated by
Clostridium sensu stricto 5 (8,7%) and
Bacillus (4,3%). Remarkably, the sample supplied 10 exclusive or nearly exclusive OTUs with more than 10 reads, among them
Dethiosulfatibacter, Providencia, Meiothermus, Myroides, Nitrosococcus, Paenalcaligenes and
Alkalibacter. Dethiosulfatibacter is a sulfate and thiosulfate-reducing organism found in coastal marine sediment [
95].
Meiothermus is known as thermophilic bacterium. Several strains have been isolated from hot springs [
96].
Alkalibacter is a anaerobic, alkaliphilic carbohydrates decomposing bacterium [
97]. With respect to the fact that the pH value and the electrical conductivity in the recent soil material are similar to the values of other samples, it could be assumed that the reads of these bacteria hint to a nutrient-rich and possibly alkaline and salt-containing environment in the ancient situation.
C137: Hz E, hearth with burned soil and clay, 2nd half of 2nd century: The sample is strongly dominated by Acinetobacter (49%). 15 specific OTUs with more than 10 reads have been found in this sample. This set includes the sulphate-reducing genera
Desulfobulbus [
98] and the pigment-producing genera
Janthionbacterium [
99] and
Vogesella [
100]. Other OTUs as
Peptoniphilus, Haemophilus and
Treponema are known for metabolization of amino acids and proteins or are pathogens for plants or animals [
101].
C139: Hz E, hearth, 2nd half 2nd century: The bacterial community is very strongly dominated by
Nocardioides (31%). Exclusively found OTUs are
Sporomusa, Granulicatella and
Thermodesulfovibrio. Species of the genus
Granulicatella are known for metabolizing different amines and alkohols [
102].
Thermodesulfovibrio is a sulphat-reducing thermophilic bacterium [
103].
C147: Hz E, hearth, red burned soil and clay from hearth floor, 2nd half 2nd century:
Nocardioides (19,5 %) is the dominating OTU. Only three specific OTUs have been observed in the sample. One of them,
Garicola was first isolated from a highly salted fermented shrimp food [
104] and could indicate residues of salt and fish – possibly in the context of garum, a fish sauce which was very popular in antiquity.
C150: Hz E, soil fill in a courtyard, 2nd half of 2nd century: The bacterial community of this sample is strongly dominated by Acinetobacter (25.5%). In addition,
Ralstonia (12.4%) and
Aquabacterium (10.7%) are also highly abundant. In contrast, some OTUs frequently highly abundant in most other samples as
Nocardioides, Myxococcota, Bacteriap25, Burkholderia TRA3-20 and
Chloroflexi KD4-96 show only low abundances in C150. With 0.4% Bacillus shows also a comparatively low presence. The ratio of reads to OTUs with ten or more reads (544) is the highest of all samples, which means that the sample shows a comparatively low diversity (the average of this ratio over all samples is 234). Only two specific OTUs have been found. One of them is
Kinneretia, a strictly aerobic bacterium originally isolated from a fresh water lake [
105].
C162: Hz E, Street, gravel fill and street surface, 2nd half of 2nd century: The bacterial community is dominated by
Pseudonocardia (11%). The soil material supplied 13 specific OTUs, among them
Flexilina, Polycladomyces, Actinotalea und
Cloacibacterium. These OTUs seem to be an echo of a soil situation with a high load of seawage or faeces, organic waste as starch, and enhanced ion concentration.
Flexilinea was isolated from methanogenic sludge from treating wastewater with a high starch-content [
106]
Polycladomyces is thermophilic bacterium firstly isolated from sea water [
107].
Actinotalea was isolated from seawater, too [
108].
Cloacibacterium is an anaerobic bacterium isolated from seawage [
109].
C165: Hz E, Road substructure (excluding the surface of use) directly below C162, 2nd half of 2nd century: The sample is marked by Nocardioides (28.5%) and Pseudonocardia (20.6%) as strongly dominating genera. In strong contrast to the street horizon directly above (C162), two specific OTUs with more than 10 reads – Acidicapsa and Asanoa - were found, only. This observation agrees with the fact that the total number of reads between sample C162 and C165 are similar (about 35,000) whereas the number of types is rather different (308 in sample C162, but only 157 different OTUs in C165). Obviously, the different sizes of the spectra of “sample-specific” types indicate a strong difference between the character of the fill directly underneath the street and the street surface itself in the ancient situation.
C169: Hz F, Clayey fill in a courtyard, deposited around 120 AD.: The bacterial community is dominated by Nocardioides (8 %), but there is a comparatively high abundance of Zixibacteria (4.1 %), too. In contrast to other samples, the analysis supplied more than 20 exclusive OTUs with less than 10 reads, but no exclusive types with ten reads or more.
C172: Hz F, clayey fill above a hearth, deposed after the hearth’s abandonment around 120 AD.: The bacterial community is dominated by
Aeromicrobium (12.6 %). In addition
Bacillus (6.1 %) and
Nocardioides (5.1 %) are highly abundant, too. Sample C172 was taken in the vicinity of the hearth-related samples C137, C147, and C178. It was marked by three specific OTUs,
Thermosediminibacter, Glaciihabitans and
Saliterribacillus. Two of them are particularly interesting because they hint to formerly enhanced soil salinity. Thermosediminibacter is an anaerobic and thermophilic organism isolated from deep sea sediment [
110].
Saliterribacillus was first described as a halophilic bacterium isolated from a hypersaline lake [
111]. The mentioned bacteria might reflect the nearness of hearth and enhanced salt concentration by ashes.
C177: Hz F, residues of a cupola oven and its destruction debris, around 120 AD.: As C172 it is dominated by Aeromicrobium (21.8 %). In addition, Nocardioides (6.5 %) and Pseudonocardia (5.5 %) are highly abundant, too. 11 reads of the Spirochaetae bacterium Leptospiraceae are the only hint of exclusivity of this sample. Species of this family are known as pathogens for mammals and man.
C178: Hz F, from the immediate vicinity of the cupola oven C 177, around 120 AD.: The bacterial community is dominated by Nitrososphaeraceae (9.1 %). 15 reads of Actinomarinales were observed, an OTU which is also present in sample C303, whereas clear exclusive OTUs are missing.
C190: Hz F: from street fill and street surface, about middle of the 2nd century AD.: The bacterial community is dominated by
Nocardioides (10.4 %). The
Crenarchaeota bacterium
Cand. Nitrososphaera (4.9 %) and
Myxococcota bacteriap25 (4.2 %) are highly abundant, too. The sample is marked by a few exclusive types, for example the two alphaproteobacteria
Shinella and
Ancylobacter. Shinella was isolated from anaerobic sludge [
112].
Ancyclobacter is able to decompose kerosene and other hydrocarbons [
113]. The last one might be interpreted to indicate an exposition to oil.
C218: Hz G: fill of a barbecue pit, around 120 AD.: Cand Nitrosphaera (6.3 %), Kryptonales BSV 26 (6.5 %) and Myxococcota bacterap25 (5.6%) are the three dominating OTUs. The 16S rRNA-reflected bacterial communities of samples C218 and C219 have a lot of similarities distinguishing them from all other samples. Besides these OTUs, there are some “sample-specific” OTUs, too. Erythrobacter is the only OTU of the barbecue pit sample C218 with more than 10 reads which appears neither in sample C219 nor in any other sample.
C219: Hz G: Coal sample from fill in barbecue pit (C218), around 120 AD.:
Myxococcota bacteriap25 with 5.2 % and uncultivated
Solimonadaceae are the dominating OTUs of the coal sample. This sample supplied eight “exclusive” OTUs with more than 10 reads among them
Colwellia, a deep sea bacterium [
114] and a strain of the sulphate-reducing order
Desulfobacterales [
115]. Both samples C218 and C219 contain the genus
Desulfitibacterium which was first described by a strain from lake sediment and is able to metabolize chloraromates [
116].
C223: Hz G, soil fill in courtyard, around 100 AD.: The bacterial community is dominated by Bacillus (9.4 %) and to a lower amount by
Paenibacillus (4.8 %) and
Cand. Nitrosphaera (4.4 %).
Fluviicola and
Oceanisphaera are specific OTUs.
Fluviicula was found first in a freshwater environment [
117]), whereas the halophilic bacterium
Oceanisphaera was originally isolated from the sea bottom [
118].
C231: Hz H, small hearth, red burned, fire-hardened hearth floor, 70−90 AD.: The bacterial community is dominated by Nocardioides (10.6 %) and Aeromicrobium (11.5 %). Besides 10 reads of the iron-oxidizing thermophilic and acidophilic bacterium Acidimicrobium, there are no further hints to specific OTUs. The features of iron oxidation and thermophilicity obviously match the characteristics of a fire place.
C232: Hz H, ash from hearth C231, 70−90 AD.: The bacterial community is strongly dominated by Lysinibacillus (25.1 %). In addition, Aeromicrobium (9.8 %) and Bacillus (13.3%) are also highly abundant genera. The ratio of reads to OTUs with ten or more reads (451) is the second highest of all samples, what means the sample shows a comparatively low diversity. The place shows two exclusive OTUs of Proteobacteria with 20 and 37 reads, resp.
C248: Trench M07, context 01, disturbed material, refill of the archaeological excavation of 1905: The sample is dominated by Nitrososphaeraceae (8.5 %), Bacillus (6.8 %) and Paenibacillus (5.6 %). The sample showed a comparatively high number of OTUs in total (783; 313 with ten or more reads) at a moderate total number of reads (43,777), which can be described as a high alpha-diversity. This sample shows the highest number of relations with other samples by signature-like patterns of lower abundant OTUs (see below). This observation can be interpreted as a strong indicator for the fact, that a considerable part of lower abundant OTUs reflects the local conditions in the ancient situation and conserved this information after mixing during the excavation of 1905. The sample supplied 37 exclusive OTUs indicated from sequencing with only one or a few reads. One OTU, only, (Cand. Abawacabacteria) is represented by 10 reads. Thus, this sample is marked by negligible exclusivity for OTUs with clear representation, but seems to show a high background noise of very low abundant types. This feature corresponds well to the above expressed assumption, that the sample reflects a mixing of different soils conserving important aspects of their ancient specific environmental information.
C263: Trench M07 context 06, fine grained, sandy alluvium underneath the deepest anthropogenic stratum, reference sample, no human interference: The bacterial community is dominated by
Pseudonocardia (19.4 %) and
Bacillus (17.8 %).
Acinetobacter (8.5 %),
Exiguobacterium (6 %) and
Nocardioides (5.9 %) are also well represented, as well as Ralstonia (3.9 %) and
Pseudomonas (2.9 %). It should be remarked here, that some other OTUs which are dominating or highly abundant in several other samples are comparatively low in C263. This concerns
Aeromicrobium (0.05 %),
Paenibacillus (0.8 %) and
Myxococcota bacteriap 25 (0.5 %). C263 is marked by a comparatively low number of total reads (27,432) and OTUs (164; 101 with ten or more reads).
Occallatibacter – a genus originally isolated from samples from the Namibian savannah and a river bank there [
119] − is the only exclusively proved genus of C263, indicating that this sample is not distinguishable by special low abundant types from the other samples. Vice versa, this could be interpreted in the way to assuming that higher numbers of exclusively found OTUs in other samples indicate their specificity reflecting the ancient environmental situation and distinguish them from the marchsand.
C266: Trench M07 context 07, burnt debris from al large refuse pit, probably first half 2nd century: The bacterial community is strongly dominated by
Aeromicrobium (22.2 %) and
Limnobacter (16.3 %). The sample shows low indication of specificity:
Desmospora was found by 54 reads and is present in C303 as the only other sample.
Desmospora was first described from the sputum of a patient with suspected tuberculosis [
120].
C282: Hz H, 70-90 AD.: soil fill directly underneath the hearth C232, 70−90 AD.: The bacterial community is dominated by Pseudomonas (9.2 %) and Nocardioides (6.4 %). The sample showed no exclusive OTUs, but it has to be remarked that the sequencing result for this sample can hardly be compared with the other samples because very low numbers of only 109 reads in total and 67 OTUs had been proved.
C283: Hz H, soil fill west of hearth (C232), 70−90 AD.: The bacterial community is dominated by
Limnobacter (9.3 %),
Nitrososphaeraceae (6.1 %),
Paenibacillus (5.6 %) and uncultivated
Anaerolineaceae (5.3 %).
Persicitalea (11 reads) and
Lachnospiraceae UCG-009 (13 reads) are present exclusively in this sample
. Persicitalea is a aerobic organism and was first isolated from seawater [
121].
C286: soil fill, Hz H, 70−90 AD.: The bacterial community is dominated by Nitrososphaeraceae (9 %) and Nocardioides (8.2 %). In addition, Bacillus (7.4 %) and Cand. Nitrosphaera (6.5 %) are also well represented. The sample supplied some exclusively found OTUs represented by less than ten reads, but showed no exclusive OTUs with ten reads or more.
C288: levelling fill underneath street surface layer, Hz, H, 70-90 AD.: The bacterial community is dominated by
Nocardioides (6.8 %),
Cand. Nitrosphaera (6.7 %) and
Paenibacillus (5.1 %). The sample supplied six exclusive or nearly exclusive OTUs, among them
Kaistia (18 Reads),
Ehrlichia (10 reads) and
Belnapia (14 reads).
Ehrlichia is known as intracellular parasite and pathogen for animals and humans [
122].
Kaistia is an aerobic bacterium first found in a stream with industrial waste in Korea [
123].
Belnapia was found in a biological soil crust and is an aerobic bacterium, too [
124].
C295: Hz A, collapse horizon, partly disturbed by modern ploughing, early 2nd half 4th century: The bacterial community is moderately dominated by Nocardioides (6.5 %) and Bacillus (6.9 %). The sample supplied 37 exclusively found OTUs represented by less than ten reads, but showed no exclusive OTUs with ten reads or more. The high number of exclusive OTUs with very low read numbers is an interesting analogon to sample C248 and could have to do with the origin of the sample soil from a former mixing of different ancient soil components.
C296: Hz A, fill and ancient surface of use, 2nd half of 4th century: The bacterial community is moderately dominated by
Nocardioides (7.8 %) and
Bacillus (5.1 %), too. The sample is marked by four specific OTUs, among them the
Gammaproteobacterium Herminiimonas and both
Actinobacteria, Plantactinospora and Krasilnikoviella. The latter one was described from a mural painting in the stone chamber of a Japanese tomb tumulus from about 700 AD [
125].
C297: Hz B, fill and surface of use in the courtyard, about 1st half of 4th century: The bacterial community is stronger dominated by Nocardioides (12%) and Bacillus (15%). C297 supplied no exclusive OTU with ten or more reads.
C298: Hz C, fill and surface of use in the building south of courtyard C297, about 2nd half of 3rd century: The bacterial community is dominated by Nocardioides (25.5 %). Bacillus (9.8 %) is the second highest abundant genus. In addition, Pseudoarthrobacter showed a high abundance (6.2 %). C298 supplied Rhodobacter HMB 11 as only exclusive OTU with ten or more reads.
C299: Hz C, fill and surface of use in the building south of the courtyard, about 2nd half of 3rd century: The bacterial community is very strongly dominated by Acinetobacter (29.3 %). Bacillus (10 %) is the second highest abundant genus, too. C299 supplied no exclusive OTU with ten or more reads.
C300: Hz C, fill and surface of use in the courtyard north of building C299, about 2nd half of 3rd century: The bacterial community is overwhelmingly dominated by Exiguobacteria (32 %) and Bacillus (16.4 %). C300 supplied no exclusive OTU with ten or more reads.
C303: Trench M06 context 06, Soil filland surface of use, post earthquake 360 AD.: The bacterial community is dominated by Aeromicrobium (9.7 %). The sample supplied no exclusive OTU with ten or more reads.
C306: trench M06 context 08, levelled rubble fill, post earthquake 360 AD.: The bacterial community is dominated by Nocardioides (7.3 %). In addition, Bacillus (5.8 %), Paenibacillus (4.1 %) and Aeromicrobium (4.4 %) are present in significant amounts as well. C306 supplied no exclusive OTU with ten or more reads.
C307: trench M06 context 10, earth fill beneath caementitium floor, probably 3rd century: The bacterial community is dominated by Bacillus (14.4 %). The hydrogen producing anaerobic bacterium
Acetobacteroides [
126] is the only exclusive OTU with more than ten reads present in this sample. Nearly as rarely documented in the samples presented here are
Anaerococcus [
127] and
Micrococcus (13 reads in C139).
C315: trench M06 context 13, levelled rubble fill, post earthquake 360 AD.: The bacterial community is dominated by Aeromicrobium (7.4 %). The sample supplied no exclusive OTU with ten or more reads.
C325: trench M06 context 16, clayey surface of use, post earthquake 360 AD.: The bacterial community is dominated by
Bacillus (8.8 %). The sample supplied two nearly exclusive OTUs:
Pectinophilus group of
Lachnospiraceae (35 reads) and
Algoriphagus (60 reads). The latter was isolated from from sea ice and from saline lake cyanobacterial mats [
128].
C330: trench M06 context 20, furnace floor surface in praefurnium of hypocaustum, around 360 AD.: The bacterial community is dominated by
Nocardioides (6.2 %). C330 showed eight exclusive or nearly exclusive OTUs with ten or more reads, among them uncultured
Arcobacteraceae (18 reads),
Chitinophagaceae UTBCD1 (15 reads),
Kordiimonas (14 reads), uncultured
Proteinivoracales (13 reads),
Cand. Neoehrlichia (13 reads), uncultured
Cellvibrionaceae (12 reads),
Roseiarcus (12 reads) and
Porphyrobacter (10 reads).
Kordiimonas was isolated from marine sediment and was found to be able to degrade polycyclic aromatic hydrocarbons [
129].
Roseiarcus is a pigmented microaerophilic bacterium first isolated from a methanotrophic microorganismic consortium [
130]. Its appearance would fit to conditions in residues of wood or other organic material and low oxygen content in the local environment inside the hypocaustum.
Porphyrobacter was found in freshwater and is a bacteriochlorphyll synthezising microorganism [
131].
C341: trench M06 context 24, lower furnace floor beneath C330, early 4th century: The bacterial community is dominated by (11.5 %). In addition,
Nocardioides (8.2 %),
Polycyclovorans (4 %) and
Polaromonas (5.2 %) are particularly abundant. -
Renibacterium, a sub-species of
Actinobacteria, is nearly exclusive in sample C341.
Renibacterium was first described as a microorganism causing kidney diseases in fish [
132].
C347: trench M06 context 30, lowest furnace floor underneath C341, 3rd century: The bacterial community is dominated by Aeromicrobium (11.6 %) and Limnobacter (10 %). A strain of Vampirovibrionaceae was exclusively present in sample C347.